tag:blogger.com,1999:blog-1202568509879946472024-03-13T14:35:23.833-07:00Protein Sequence and Structure BioinformaticsAhttp://www.blogger.com/profile/14312808974629818240noreply@blogger.comBlogger77125tag:blogger.com,1999:blog-120256850987994647.post-54665728018428254632014-04-25T06:49:00.002-07:002014-04-25T06:50:31.726-07:00Systematic Detection of Internal Symmetry in Proteins Using CE-SymmIn our latest paper, "<i><a href="http://www.sciencedirect.com/science/article/pii/S0022283614001557">Systematic Detection of Internal Symmetry in Proteins Using CE-Symm</a></i>", we are taking a look at how internal symmetry in proteins is related to protein function. A large number of proteins have symmetry not only in their biological assemblies, but also within their tertiary structures. To investigate the question of how internal symmetry evolved, how symmetry and function are related, and the overall frequency of internal symmetry, we developed a new algorithm that can detect pseudo-symmetry within tertiary structures of proteins. Our results indicate that more domains are pseudo-symmetric than previously estimated. We establish a number of recurring types of symmetry–function relationships and describe several characteristic cases in detail.<br />
<br />
Read more over at <a href="http://www.sciencedirect.com/science/article/pii/S0022283614001557">JMB</a>.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://origin-ars.els-cdn.com/content/image/1-s2.0-S0022283614001557-gr1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://origin-ars.els-cdn.com/content/image/1-s2.0-S0022283614001557-gr1.jpg" height="320" width="291" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<i>Several protein domains with internal symmetry that CE-Symm detects. Coloring is by symmetry unit.</i></div>
<div class="separator" style="clear: both; text-align: center;">
<i><br /></i></div>
<div class="separator" style="clear: both; text-align: center;">
<i><br /></i></div>
<br />
<div>
<br /></div>
Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-83476462330883102202014-03-25T15:52:00.000-07:002014-03-25T15:52:34.876-07:00BioJava 3.0.8 released<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
<div>
BioJava 3.0.8 was released on March 25th 2014 and is available from</div>
<div>
<a href="http://biojava.org/wiki/BioJava:Download" style="color: #1155cc;" target="_blank">http://biojava.org/wiki/<wbr></wbr>BioJava:Download</a> as well as from the</div>
<div>
BioJava maven repository at <a href="http://www.biojava.org/download/maven/" style="color: #1155cc;" target="_blank">http://www.biojava.org/<wbr></wbr>download/maven/</a></div>
<div>
<br /></div>
<div>
<div>
This release would not have been possible without contributions from</div>
<div>
13 developers, thanks to all for their support!</div>
</div>
<div>
<br /></div>
<div>
BioJava 3.0.8 includes a lot of new features as well as numerous bug fixes and improvements.</div>
<div>
<br /></div>
<div>
<i>New Features:</i></div>
<div>
<ul>
<li> new Genbank writer</li>
<li> new parser for Karyotype file from UCSC</li>
<li> new parser for Gene locations from UCSC </li>
<li> new parser for Gene names file from <a href="http://genenames.org/" style="color: #1155cc;" target="_blank">genenames.org</a></li>
<li> new module for Cox regression code for survival analysis</li>
<li> new calculation of accessible surface area (ASA)</li>
<li> new module for parsing .OBO files (ontologies)</li>
<li> improved representation of SCOP and Berkeley-SCOP classifications</li>
</ul>
</div>
<div>
</div>
<div>
For a detailed comparison see here:</div>
<div>
<a href="https://github.com/biojava/biojava/compare/biojava-3.0.7...biojava-3.0.8" style="color: #1155cc;" target="_blank">https://github.com/biojava/<wbr></wbr>biojava/compare/biojava-3.0.7.<wbr></wbr>..biojava-3.0.8</a></div>
<div>
<br /></div>
<div>
For the next release we are planning some refactoring and removal of code that has been deprecated for a long time. As such the next release will be named 3.1.0.</div>
<div>
<br /></div>
<div>
About BioJava:</div>
<div>
<br /></div>
<div>
BioJava is a mature open-source project that provides a framework for</div>
<div>
processing of biological data. BioJava contains powerful analysis and</div>
<div>
statistical routines, tools for parsing common file formats, and</div>
<div>
packages for manipulating sequences and 3D structures. It enables</div>
<div>
rapid bioinformatics application development in the Java programming</div>
<div>
language.</div>
<div>
<br /></div>
<div>
Happy BioJava-ing,</div>
</div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
<br /></div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
Andreas</div>
Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-2926819610987627202013-09-04T23:03:00.001-07:002013-09-04T23:09:59.139-07:00RCSB PDB September 2013 releaseThis week we released the latest <a href="http://www.rcsb.org/">RCSB PDB web site update</a>. <div>
<table>
<tbody>
<tr>
<td><a href="http://www.rcsb.org/pdb/general_information/releases/1308_images/Symmetry_woBox.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;">
<img border="0" src="http://www.rcsb.org/pdb/general_information/releases/1308_images/Symmetry_woBox.png" /></a>
</td>
<td><a href="http://www.rcsb.org/pdb/general_information/releases/1308_images/DrugsIcon_woBox.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://www.rcsb.org/pdb/general_information/releases/1308_images/DrugsIcon_woBox.png" /></a>
</td>
<td><a href="http://www.rcsb.org/pdb/general_information/releases/1308_images/SymmetryAxes_woBox.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://www.rcsb.org/pdb/general_information/releases/1308_images/SymmetryAxes_woBox.png" /></a>
</td>
</tr>
</tbody></table>
The main new features are:<br />
<br />
- New tools to search for drugs and drug targets<br />
- Improved interface for 3D visualisation using Jmol/JSmol<br />
- An update to the representation of protein symmetry and stoichiometry.<br />
- Improvements when performing sequence searches.<br />
<br />
Jesse redesigned our <a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1308">what's new page</a> and made it look really nice, take a look to see all the details!<br />
<br />
<br />
<br />
<br /></div>
Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-73053775390662768472013-08-01T11:35:00.000-07:002013-08-01T11:35:38.408-07:00Workshop on Sustainable Software for Science: Practice and ExperiencesInterested in sustainability of scientific software?<br />
<br />
First Workshop on Sustainable Software for Science: Practice and<br />
Experiences (WSSSPE)<br />
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)<br />
<a href="http://wssspe.researchcomputing.org.uk/">http://wssspe.researchcomputing.org.uk/</a><br />
<div>
<br /></div>
<br />Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-22345915613534156262013-03-19T07:45:00.000-07:002013-03-19T07:45:04.088-07:00Trendspotting in the Protein Data BankOur most recent article has become publicly available. It describes some of the trends that we can observe in the Protein Data Bank:<br />
<br />
<br />
<div style="margin-left: 24pt; text-indent: -24.0pt;">
<a href="http://www.sciencedirect.com/science/article/pii/S0014579313000240">Trendspotting in the Protein Data Bank. </a><i>FEBS Letters</i>, (0). <span style="text-indent: -24pt;">Berman, H. M., Coimbatore Narayanan, B., Costanzo, L. D., Dutta, S., Ghosh, S., Hudson, B. P., Lawson, C. L., et al. (n.d.). </span><span style="text-indent: -24pt;">doi:http://dx.doi.org/10.1016/j.febslet.2012.12.029</span></div>
<br />
<br />
<a href="http://www.sciencedirect.com/science/article/pii/S0014579313000240">http://www.sciencedirect.com/science/article/pii/S0014579313000240</a>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-9830268622256185232013-03-08T07:46:00.001-08:002013-03-08T07:56:23.576-08:00Spring 2013 release of RCSB PDBThis week we released the spring 2013 release of the RCSB PDB's website. This release was a lot of work and we added a ton of new features and improvements. Here my wrap-up of some of our highlights. For a full listing <span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;">see the </span><a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1301" style="background-color: white; border: 0px; color: #336699; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; font-weight: bold; line-height: 18px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none;">What's New page for more features and examples</a><span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;">.</span><br />
<br />
<h3>
Protein Symmetry and Stoichiometry</h3>
The calculation of protein symmetry and stoichiometry is one of the major features of this release. The goal is to better describe biological assemblies of proteins according to some of their characteristics.<br />
<br />
<span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;"><b>Symmetry</b> refers to the point group symmetry of a protein complex. P</span><span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;">rotein complexes with quaternary structure can have rotational symmetry belonging to the point groups: cyclic (Cn), dihedral (Dn), tetrahedral (T), octahedral (O), or icosahedral (I).</span><span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;"> </span><br />
<span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;"><br /></span>
<br />
<span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;">The </span><b style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;">stoichiometry</b><span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;"> of a protein complex represents the composition of its subunits. For example, the biological assembly of hemoglobin has two alpha and two beta subunits, represented by the formula A2B2.</span><br />
<span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;"><br /></span>
<span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;">Here a few examples:</span><br />
<br />
<span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;"><br /></span>
<span style="background-color: white; color: #222222; font-family: verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 18px;"><br /></span>
<span class="h3">The <a href="http://www.rcsb.org/pdb/explore/jmol.do?structureId=4H56&bionumber=1">Crystal structure of the Clostridium perfringens NetB toxin in the membrane inserted form</a></span><br />
has a <b>cyclic symmetry of C7 </b>and is formed by a homo-7-mer (A7)<br />
<br />
<br />
<table><tbody>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjgLmj9q6WuyCyRGf-JdaN9pWtQ9I6mJkD1PLIqr3jJ1Ybie3yEsA2MWjxCrRaYngZwvKO1oopqny6gw_jEgJUslNDeFIRmmfBEj9YrgIdoyMKp7ehZyjJKDt2Jbrob3wAyquKFqylIEjI/s1600/Screen+Shot+2013-03-07+at+8.03.58+AM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="198" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjgLmj9q6WuyCyRGf-JdaN9pWtQ9I6mJkD1PLIqr3jJ1Ybie3yEsA2MWjxCrRaYngZwvKO1oopqny6gw_jEgJUslNDeFIRmmfBEj9YrgIdoyMKp7ehZyjJKDt2Jbrob3wAyquKFqylIEjI/s200/Screen+Shot+2013-03-07+at+8.03.58+AM.png" width="200" /></a>
</td><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8cuQksIRWeNhgPbaIXSrrVbgHUA7i059gXzn1TmIFrhKoEDhCEEtIkbvrVQg8XVwpVMA9zU5rAoPgGQRcgiLgToLDdqjH2Kezcx9z5ElS4yZQk0ArDhxLefRqm8vds2zJYyrxyxzUmro/s1600/Screen+Shot+2013-03-07+at+8.02.34+AM.png" imageanchor="1" style="clear: left; display: inline !important; float: left; margin-bottom: 1em; margin-right: 1em; text-align: center;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8cuQksIRWeNhgPbaIXSrrVbgHUA7i059gXzn1TmIFrhKoEDhCEEtIkbvrVQg8XVwpVMA9zU5rAoPgGQRcgiLgToLDdqjH2Kezcx9z5ElS4yZQk0ArDhxLefRqm8vds2zJYyrxyxzUmro/s200/Screen+Shot+2013-03-07+at+8.02.34+AM.png" width="200" /></a>
</td></tr>
</tbody></table>
<br />
The <a href="http://www.rcsb.org/pdb/explore/jmol.do?structureId=4AP9&bionumber=1">Crystal structure of phosphoserine phosphatase from T. onnurineus</a> has <b>Dihedral</b> - D4 symmetry and is formed by a homo-8-mer (A8)<br />
<table><tbody>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxFyp-FZ7ZDFSItZlP5Yc97XUgPbn-_zXwNorkc3wMRDkLcgYQcFyeHVOIUiWHRVoOsHxJVma0Y63OCKc0afQ8qKevyYRrcxqi1tdErh_dmVTlSCjQlJ68lszULt319XCiGiq-cjYR1uc/s1600/Screen+Shot+2013-03-07+at+23.21.10.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxFyp-FZ7ZDFSItZlP5Yc97XUgPbn-_zXwNorkc3wMRDkLcgYQcFyeHVOIUiWHRVoOsHxJVma0Y63OCKc0afQ8qKevyYRrcxqi1tdErh_dmVTlSCjQlJ68lszULt319XCiGiq-cjYR1uc/s200/Screen+Shot+2013-03-07+at+23.21.10.png" width="198" /></a>
</td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgbqPbRSM0fkC6Hs5LRyZtkZMBsjSCUGcly0i6OefeXEhc5QMOEo3sf5BZjUtBV2_akDbgnbvw5hUmdT1xL06Dc-vq4LjL5zcAc-1z1FYpU6A8wAMeDwLOhx56Suzo39aY9uRxjRgu-v8Q/s1600/Screen+Shot+2013-03-07+at+23.20.50.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="199" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgbqPbRSM0fkC6Hs5LRyZtkZMBsjSCUGcly0i6OefeXEhc5QMOEo3sf5BZjUtBV2_akDbgnbvw5hUmdT1xL06Dc-vq4LjL5zcAc-1z1FYpU6A8wAMeDwLOhx56Suzo39aY9uRxjRgu-v8Q/s200/Screen+Shot+2013-03-07+at+23.20.50.png" width="200" /></a> </td></tr>
</tbody>
</table>
The <a href="http://www.rcsb.org/pdb/explore/jmol.do?structureId=4EME&bionumber=1">Plasmodium falciparum malaria aminopeptidase</a> has <b>Tetrahedral</b> symmetry and is a homomer composed of 12 chains.<br />
<div>
<br /></div>
<table><tbody>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSUKPMD_ztVx2-nkyT3vG6iOyVdXOlZWSoGZNYBH7Ib53Fo5SSAnsrQKiUu8Jqi0vgsQY7eo7XgG2a7mZb_0jxipt6QIy3odPIKqq-YDDlkrJYSdXrf6NsaTsn_rqSPFSw6jD2X1Nixps/s1600/Screen+Shot+2013-03-07+at+23.43.33.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="197" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSUKPMD_ztVx2-nkyT3vG6iOyVdXOlZWSoGZNYBH7Ib53Fo5SSAnsrQKiUu8Jqi0vgsQY7eo7XgG2a7mZb_0jxipt6QIy3odPIKqq-YDDlkrJYSdXrf6NsaTsn_rqSPFSw6jD2X1Nixps/s200/Screen+Shot+2013-03-07+at+23.43.33.png" width="200" /></a>
</td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEzi0lLD8kNfkTLQtY6LfR_cYBfqee-rmUbRPnyXC1_WVeTG8hA25B3uF_9WmFd3dl5VvAE2iWmC1kHQEJS-9VVYqzLzlNX2B_pgSzHAlZxx3R5y1oWia9NwuAReyqgA1gjNyoPpCwnrs/s1600/Screen+Shot+2013-03-07+at+23.43.19.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEzi0lLD8kNfkTLQtY6LfR_cYBfqee-rmUbRPnyXC1_WVeTG8hA25B3uF_9WmFd3dl5VvAE2iWmC1kHQEJS-9VVYqzLzlNX2B_pgSzHAlZxx3R5y1oWia9NwuAReyqgA1gjNyoPpCwnrs/s200/Screen+Shot+2013-03-07+at+23.43.19.png" width="200" /></a>
</td></tr>
</tbody></table>
<div>
<br />
<a href="http://www.rcsb.org/pdb/explore/jmol.do?structureId=4DAS&bionumber=1">Ferritin</a> has <b>Octahedral</b> symmetry and is a Homo 24-mer<br />
<br />
<table><tbody>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg4_ImrNNjQsM8Ae_MlPVndC9OmC0PTh1MklJrox4DFmXMIMI5Erw2pOOD7lxgQAC8IBe8pMpwguosDxeaH4zoD3tndXyQoskmgPexiwtQSjPsGO9221jiCoaJKVj5p4OXitJGG2tkzDVc/s1600/Screen+Shot+2013-03-07+at+23.48.23.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg4_ImrNNjQsM8Ae_MlPVndC9OmC0PTh1MklJrox4DFmXMIMI5Erw2pOOD7lxgQAC8IBe8pMpwguosDxeaH4zoD3tndXyQoskmgPexiwtQSjPsGO9221jiCoaJKVj5p4OXitJGG2tkzDVc/s200/Screen+Shot+2013-03-07+at+23.48.23.png" width="200" /></a>
</td><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjH2S0i94bE5s2AAZD_w7fRWSHOqhUx3xsURwmIIc6NitbyThM_n0bdvXoXEtP0yKmmgl3jh9mHMbSjwjBBIpGQ_CcS1nQcmRgjpuej5O6ivOBL_o7ujUqKTFSNQVGXB5JJ2_B1u6L1En8/s1600/Screen+Shot+2013-03-07+at+23.47.55.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjH2S0i94bE5s2AAZD_w7fRWSHOqhUx3xsURwmIIc6NitbyThM_n0bdvXoXEtP0yKmmgl3jh9mHMbSjwjBBIpGQ_CcS1nQcmRgjpuej5O6ivOBL_o7ujUqKTFSNQVGXB5JJ2_B1u6L1En8/s200/Screen+Shot+2013-03-07+at+23.47.55.png" width="197" /></a></td></tr>
</tbody></table>
<br />
The <a href="http://www.rcsb.org/pdb/explore/jmol.do?structureId=1ZBE&bionumber=1">Foot-and Mouth Disease Virus</a> has <b>Icosahedral</b> symmetry and is formed by a Hetero-240 mer with the a A60B60C60D60 stoichiometry.<br />
<div>
<br /></div>
<table><tbody>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhoQtI00vIPdhsD8gT0IUzoX-DWxuVFRr4OznGaNtHcx-8oEu2Y6G5sYVtQ_Ni5nyhFlQmG7pBPQ2tglmff-HaOy4BkRXaLHQZzsqsg1AVBNKQwnzBVgwwM6aSFnxS2OvJ1MZXs7utupvA/s1600/Screen+Shot+2013-03-07+at+23.37.32.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="199" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhoQtI00vIPdhsD8gT0IUzoX-DWxuVFRr4OznGaNtHcx-8oEu2Y6G5sYVtQ_Ni5nyhFlQmG7pBPQ2tglmff-HaOy4BkRXaLHQZzsqsg1AVBNKQwnzBVgwwM6aSFnxS2OvJ1MZXs7utupvA/s200/Screen+Shot+2013-03-07+at+23.37.32.png" width="200" /></a>
</td><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEipKsAHPUyAYoFKbstI56v5un7OlnHXYH0nO-WH0IFJEwZaAFSLgdk9e5oQuiZVBRwopg7AnSaZL1qVOvzevFXTIGnt9xvUYIZnBjiOKQjttZTyUp8zGHCeLayplcBIqbd5m0fCtTeOdXo/s1600/Screen+Shot+2013-03-07+at+23.36.22.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEipKsAHPUyAYoFKbstI56v5un7OlnHXYH0nO-WH0IFJEwZaAFSLgdk9e5oQuiZVBRwopg7AnSaZL1qVOvzevFXTIGnt9xvUYIZnBjiOKQjttZTyUp8zGHCeLayplcBIqbd5m0fCtTeOdXo/s200/Screen+Shot+2013-03-07+at+23.36.22.png" width="198" /></a></td></tr>
</tbody></table>
<div>
<br />
<div>
<br /></div>
<div>
Tip: Enable the <i>Axes</i> and <i>Polyhedron </i>options on the Jmol page to get a better understanding of the composition of the protein.<br />
<br />
<h3>
Biologically Interesting Molecules</h3>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.rcsb.org/pdb/general_information/new_images/1301_bird_widget.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="58" src="http://www.rcsb.org/pdb/general_information/new_images/1301_bird_widget.png" width="320" /></a></div>
<div>
</div>
<div>
<br /></div>
<div>
Various biologically interesting molecules, such as peptide-like antibiotic and inhibitor molecules are being annotated by the PDB. The latest RCSB PDB website provides better access to these data. These molecules are now search-able in the top-bar search, and we provide better reports and visualisation.</div>
<div>
<br /></div>
<div>
Example: <a href="http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=BirdQuery&name=VANCOMYCIN">All structures that contain Vancomycin</a></div>
<h3>
</h3>
<h3>
Access to Drug Targets in the PDB </h3>
<div>
For this release we integrated drug and drug target data from DrugBank (<a href="http://www.drugbank.ca/">www.drugbank.ca</a>). For example: <a href="http://www.rcsb.org/pdb/search/smart.do?smartSearchSubtype_0=ChemCompIdQuery&target=Ligand&chemCompId_0=IZP&evtc=Suggest&evta=ChemicalName&evtl=TopBar">look up Ibuprofen</a> .</div>
<div>
<br /></div>
<div>
We also provide <a href="http://www.rcsb.org/pdb/browse/jbrowse.do?t=18&useMenu=no">access to the Anatomical Therapeutic Chemical</a> (ATC) Classification System, which is used for drug classification.</div>
<div>
<br /></div>
<h3>
Better site navigation</h3>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.rcsb.org/pdb/general_information/new_images/1301_top_bar_search.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="45" src="http://www.rcsb.org/pdb/general_information/new_images/1301_top_bar_search.png" width="320" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
We have re-designed our page header and given it a cleaner and simpler feel.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<h3>
Uniprot Gene Names</h3>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOB6jl_4p7FOFjzEmWv7ISCuKdVwBA6LKX8KSS4Zqxy81qMMzYT1_yNrkUKFKC9I7pemsd_YV2WPcx-dWsBdBIuLzG6DiK07obvSF-5GTes9VtFoB5uFOEsfHV3KQfbZnEhyo_VA3oFwg/s1600/Screen+Shot+2013-03-08+at+7.33.14+AM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOB6jl_4p7FOFjzEmWv7ISCuKdVwBA6LKX8KSS4Zqxy81qMMzYT1_yNrkUKFKC9I7pemsd_YV2WPcx-dWsBdBIuLzG6DiK07obvSF-5GTes9VtFoB5uFOEsfHV3KQfbZnEhyo_VA3oFwg/s1600/Screen+Shot+2013-03-08+at+7.33.14+AM.png" /></a></div>
<div>
We added a new search function for Gene names. Proteins that can be linked to PDB via Uniprot can now be identified by their associated gene annotations.</div>
<div>
<br /></div>
<div>
<br /></div>
<h3>
SCOP track in Protein Feature View</h3>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.rcsb.org/pdb/general_information/new_images/1301_scop.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://www.rcsb.org/pdb/general_information/new_images/1301_scop.png" width="320" /></a></div>
<div>
<br /></div>
<div>
The Protein Feature View now has a new track - domain annotations from SCOP. Example: <a href="http://www.pdb.org/pdb/protein/Q27709">Obelin</a></div>
<div>
<br /></div>
<div>
This was just a quick summary of some of the new features. For a complete list, take a look at the <a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1301">What's new page</a>.</div>
<div>
<br /></div>
<div>
<br /></div>
<br /></div>
</div>
</div>
Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-64422554733503558172012-12-10T08:00:00.000-08:002012-12-10T08:00:01.823-08:00Protein Feature View goes open sourceThe source code for the <a href="http://openbioinformatics.blogspot.com/2012/10/rcsb-pdb-web-site-update-fall-2012.html">Protein Feature View</a> has been released <a href="http://andreasprlic.github.com/proteinfeatureview/">at github</a>. This allows you to incorporate the dynamic SVG graphics visualizing UniProt and PDB relationships into your own web sites. You can either use the public JSON services provided by RCSB PDB to populate the view, or display your own data (after setting up your own services).<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://raw.github.com/andreasprlic/proteinfeatureview/master/images/P06213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://raw.github.com/andreasprlic/proteinfeatureview/master/images/P06213.png" width="291" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<br />Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-84026618566699517742012-12-08T19:05:00.000-08:002012-12-08T19:34:14.435-08:00RCSB PDB's NAR paperThe manuscript describing recent developments at the RCSB PDB has been released as part of the latest Nucleic Acid Research database issue.<br />
<br />
<a href="http://nar.oxfordjournals.org/content/early/2012/11/26/nar.gks1200.full">View the manuscript at NAR</a><br />
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://nar.oxfordjournals.org/content/early/2012/11/26/nar.gks1200/F4.large.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><br class="Apple-interchange-newline" /><img border="0" height="320" src="http://nar.oxfordjournals.org/content/early/2012/11/26/nar.gks1200/F4.large.jpg" width="313" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<i>The Author Profile provides a graphical timeline on when a particular structure was released in the PDB.</i></div>
<div>
<i><br /></i></div>
<br />
<br />
Some of the highlights of this year are improvements in the following areas:<br />
<ul>
<li>Searching</li>
<ul>
<li>Better simple searches</li>
<li><a href="http://openbioinformatics.blogspot.com/2011/09/rcsb-pdb-web-site-update-this-week.html">Auto suggest provides quick access to relevant results</a></li>
<li>More advanced search options</li>
</ul>
<li>More and better tools</li>
<ul>
<li><a href="http://openbioinformatics.blogspot.com/2012/05/systematic-domain-based-structure.html">Structure alignments now domain based</a></li>
</ul>
<li>Visualization</li>
<ul>
<li>Better ligand reporting and visualisation</li>
<li><a href="http://openbioinformatics.blogspot.com/2011/12/rcsb-pdb-fall-2011-web-site-update.html">Visualisation of molecular surfaces</a></li>
</ul>
<li>Web services</li>
<ul>
<li>many new services</li>
<li>customization of reports</li>
</ul>
<li>Mobile phone app</li>
<ul>
<li>New iPhone app</li>
</ul>
<li>PDB101 educational section</li>
<ul>
<li>Structural view of biology - browse through molecule of the month articles</li>
<li>Author profiles</li>
</ul>
</ul>
<div>
Our continuous efforts to provide a structural view of biology are also reflected by an increase in our user base. The RCSB PDB web site currently hosts ∼240 000 unique visitors per month (based on the number of unique IP addresses), an increase from the 180 000 visitors last reported in 2011. </div>
Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-79770889139392285712012-12-06T14:30:00.000-08:002012-12-06T14:30:26.523-08:00Ten Simple Rules For The Open Development of Scientific SoftwareJim Procter and I drafted a new manuscript for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002802">PLOS Computational Biology</a> describing ten simple rules for the open development of scientific software. <span style="text-indent: 36pt;">Our motivation for writing this was to make the
development of open scientific software more rewarding and the experience of
using software more positive. The ten rules are intended to serve as
a guide for any computational scientist:</span><br />
<span style="text-indent: 36pt;"><br /></span>
<!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-GB</w:LidThemeOther>
<w:LidThemeAsian>JA</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
<w:UseFELayout/>
</w:Compatibility>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="276">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]-->
<!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0cm 5.4pt 0cm 5.4pt;
mso-para-margin:0cm;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:12.0pt;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-ansi-language:EN-GB;
mso-fareast-language:JA;}
</style>
<![endif]-->
<!--StartFragment-->
<!--EndFragment--><br />
<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002802">Ten Simple Rules For the Open Development of Scientific Software (article)</a><span id="goog_1741585297"></span><span id="goog_1741585298"></span><a href="http://www.blogger.com/"></a>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-51550020551509415232012-12-04T11:42:00.000-08:002012-12-04T11:42:16.565-08:00RCSB PDB is hiring<span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">The </span><a href="http://www.rcsb.org/pdb/home/home.do" style="font-family: arial, sans-serif; font-size: 13px;">RCSB PDB</a><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;"> is one of the leading biological databases with more than 240,000 unique visitors per month. </span><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">We have an open position in our team for a Lead Web Architect. The</span><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;"> position is located in beautiful </span><a href="http://en.wikipedia.org/wiki/San_Diego" style="font-family: arial, sans-serif; font-size: 13px;">San Diego</a><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;"> at <a href="http://www.ucsd.edu/">UCSD</a> .</span><br />
<br />
<span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">A detailed job description and online application form can be found at:</span><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><a href="http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_in=64091" style="background-color: white; color: #1155cc; font-family: arial, sans-serif; font-size: 13px;" target="_blank">http://jobs.ucsd.edu/bulletin/<wbr></wbr>job.aspx?cat=information&<wbr></wbr>sortby=post&jobnum_in=64091</a><br />
<br />
<span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">Qualifications:</span><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">* MS Degree in Computer Science or comparable combination of education and experience with considerable focus in </span><span class="il" style="background-color: #ffffcc; color: #222222; font-family: arial, sans-serif; font-size: 13px;">Java</span><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">EE software development.</span><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">* Established demonstrated work experience in the role of an architect and developer on medium to large size database-driven web applications using </span><span class="il" style="background-color: #ffffcc; color: #222222; font-family: arial, sans-serif; font-size: 13px;">Java</span><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;"> EE technology and standards.</span><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">* Advanced experience developing the presentation layer of a dynamic, database-driven web application using HTML, CSS, JavaScript, JavaScript Toolkits, Ajax, JSP, XML, </span><span class="il" style="background-color: #ffffcc; color: #222222; font-family: arial, sans-serif; font-size: 13px;">Java</span><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">. Experience resolving browser and cross-platform compatibility issues. Advanced experience with Struts2, Tiles, jQuery.</span><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">* Advanced experience with database design, Structured Query Language and RDBMS's such as MySQL. Expertise in web application server administration and configuration such as Tomcat.</span><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><span style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">* Established expertise in software life cycle methodologies. Experience with build tools such as Maven and Ant, and continuous integration systems such as Cruise Control. Experience with project tracking tools such as Jira.</span>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-19041556634100792442012-11-30T16:59:00.001-08:002012-11-30T16:59:55.196-08:00BioJava 3.0.5 released<br />
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
BioJava 3.0.5 has been released and is available from <a href="http://www.biojava.org/wiki/BioJava:Download" style="color: #1155cc;" target="_blank">http://www.biojava.org/<wbr></wbr>wiki/BioJava:Download</a> as well as from the BioJava maven repository at <a href="http://www.biojava.org/download/maven/" style="color: #1155cc;" target="_blank">http://www.biojava.org/<wbr></wbr>download/maven/</a> .</div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
<br /></div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
New Features:</div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
<br /></div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
- New parser for CATH classification</div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
<br /></div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
- New parser for Stockholm file format</div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
<br /></div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
- Significantly improved representation of biological assemblies of protein structures. Now can re-create biological assembly from asymmetric unit</div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
<br /></div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
- Several bug fixes</div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
<br /></div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;">
Thanks to Daniel Asarnow for contributing the CATH parser and Amr Al Hossary and Marco Vaz for their contributions to the Stockholm parser.</div>
<div>
<br /></div>
Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-26076912995174717882012-11-29T15:13:00.001-08:002012-11-29T15:15:18.067-08:00The PLOS Computational Biology Software Section<a href="http://www.ploscompbiol.org/">PLOS Computational Biology</a> has been accepting and publishing so call <i><a href="http://www.ploscompbiol.org/static/guidelines.action#software">Software Articles</a> </i>for about a year now. The articles that have been released under this category span a wide range of different topics in computational biology. In today's editorial, Hilmar Lapp and I are providing a brief overview of what has been published so far and describe some of the ideas behind the Software section.<br />
<br />
<a href="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002799">http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002799</a>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-51595406061741149822012-10-28T08:00:00.000-07:002012-10-28T08:09:09.195-07:00RCSB PDB web site update Fall 2012<h3>
New Features at the RCSB PDB web site</h3>
This week the <a href="http://www.rcsb.org/">RCSB PDB</a> released the <a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1209">latest major web site update</a>. Here a quick description of some of the new features.<br />
<br />
<h4>
Protein Feature View</h4>
One of the main new features is the new <a href="http://www.rcsb.org/pdb/protein/P04585">Protein Feature View</a>. It allows to compare the full length protein sequence, as defined by UniProt with the regions that have been determined in 3D and are available together with their coordinates from the Protein Data Bank. Besides the visualization of the PDB and UniProt relationships, the new view also adds additional annotations for a more comprehensive understanding of the protein. External data such as <a href="http://www.pfam.org/">Pfam</a> domains or regions for which Homology Models are available from the <a href="http://www.proteinmodelportal.org/">ProteinModelPortal</a> are indicated. There are also some annotations that are being calculated on the fly: Protein disorder regions, as predicted by Peter Troshin's <a href="http://www.biojava.org/">BioJava</a> implementation of <a href="http://www.ncbi.nlm.nih.gov/pubmed/15947016">RONN</a> are available as a histogram-style track. Finally, regions with increased hydrophobicity can be spotted by looking at the Hydropathy track. <br />
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.rcsb.org/pdb/help/images/featureViewQ13627.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="131" src="http://www.rcsb.org/pdb/help/images/featureViewQ13627.png" width="320" /></a></div>
<br />
The Protein Feature View is built using SVG graphics and extensively uses the <a href="http://keith-wood.name/svg.html">jQuery-SVG</a> library. Using SVG graphics for a prominently feature on the site (it is on every protein-explorer page) has become possible since the majority of all modern browsers support these types of graphics nowadays. However, there is still a number of users who are stuck with old browser versions. According to our web site traffic logs, this number is rapidly declining and we estimate that currently less than 15% of our users can't use the new view. These users won't see error messages on the protein-explorer page, thought. The graphics will simply not be visible and provide a graceful fallback to the way the page used to look before the graphics were introduced. <br />
<h4>
</h4>
<h4>
Better Pfam integration </h4>
<br />
Another new feature of this release is a better integration with <a href="http://www.pfam.org/">Pfam</a>. Pfam family names are now searchable and one can quickly lookup all protein structures related to these families. Since Pfam is used in structural genomics projects to prioritize targets for crystallization, a possible use case is to look up domains of unknown function (<a href="http://en.wikipedia.org/wiki/Domain_of_unknown_function">DUFs</a>) and whether 3D coordinates have already been determined for them. As already mentioned above, Pfam domains can be viewed as part of the new Protein Feature View. Weekly up-to-date Pfam-PDB mappings are being calculated by submitting newly released PDB entries to the HMMER3 web site. The details of this process are being described in more detail <a href="http://xfam.wordpress.com/2012/05/09/pdb-pfam-mapping/">at the Pfam blog site</a>.<br />
<br />
<h3>
Searching and Reporting </h3>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.rcsb.org/pdb/general_information/new_images/1209_poly_small.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img alt="" border="0" src="http://www.rcsb.org/pdb/general_information/new_images/1209_poly_small.png" title="RCSB PDB search now has better support for polyproteins." /></a></div>
<br />
Other improvements of this RCSB PDB web site update include search and reporting improvements. RCSB searches have been improved for better supporting poly-proteins and their sub-components (see screenshot above). There is also better support for searching drug names (and more information about drugs on the Ligand Summary page (e.g. <a href="http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=117">Lipitor</a>), coming from <a href="http://www.drugbank.ca/">DrugBank</a> . Once a search has been performed, there are now four different types of reports available for investigating the results. Besides the "<i>traditional</i>" search results there is now a "<i>condensed</i>" view, which provides a compact summary of results. The "<i>gallery</i>" provides images for the proteins that have been found in the search. A "<i>timeline</i>" gives a historic overview when proteins were released in the PDB<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.rcsb.org/pdb/general_information/new_images/1209_timeline_large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img alt="" border="0" height="268" src="http://www.rcsb.org/pdb/general_information/new_images/1209_timeline_large.png" title="The new Timeline View for search results at the RCSB PDB" width="320" /></a></div>
<br />
<br />
A full description of all the new features is (as always) available on the <a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1209">What's New Page</a>.Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-3903649085114815002012-08-10T09:00:00.002-07:002012-08-10T09:05:30.104-07:00BioJava 2012 paper published<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Today the latest BioJava paper was published, describing the BioJava version 3 series .</span><br />
<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Thanks to all developers for their contributions, it would not have been possible without them!</span><br />
<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Abstract:</span><br />
<br />
<pre><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref">http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref</a>
</span><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">PDF:</span>
<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><a href="http://bioinformatics.oxfordjournals.org/cgi/reprint/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref">http://bioinformatics.oxfordjournals.org/cgi/reprint/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref</a>
Citation:
<b>BioJava: an open-source framework for bioinformatics in 2012
</b>
<i>Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius
Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock
Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L.
Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis</i>
Bioinformatics 2012; doi: 10.1093/bioinformatics/bts494</span></pre>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-63873208179080996202012-05-21T22:04:00.002-07:002012-05-21T22:05:07.334-07:00BioJava 3.0.4 releasedBioJava 3.0.4 just hit the servers. This is mainly a bug-fix release addressing a few issues with the protein structure and the disorder modules.<br />
<br />
One new feature is that SCOP can now be either accessed from the original <a href="http://scop.mrc-lmb.cam.ac.uk/scop/">SCOP site in the UK</a> or the <a href="http://scop.berkeley.edu/">Berkeley version</a>.Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-14215752790928047182012-05-09T22:55:00.000-07:002012-05-09T22:56:08.399-07:00About Pfam and PDB mappings<span style="background-color: white; font-family: Arial, sans-serif; font-size: 13px; line-height: 18px;">Today's blog article is not going to get published here but at the Pfam blog site, where Rob Finn and I wrote about the Pfam and PDB mappings:</span><br />
<span style="background-color: white; font-family: Arial, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><br />
Does my family of interest have a determined 3D protein structure?<br />
<br />
<div>
<a href="https://xfam.wordpress.com/2012/05/09/pdb-pfam-mapping/" style="font-family: Arial, sans-serif; font-size: 13px; line-height: 18px;">https://xfam.wordpress.com/2012/05/09/pdb-pfam-mapping/</a></div>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-46935169273457319652012-05-04T09:15:00.002-07:002012-05-04T09:39:34.526-07:00Systematic domain based structure alignments at the RCSB PDBAt the <a href="http://www.rcsb.org/">RCSB PDB web site</a> we habe been providing <a href="http://openbioinformatics.blogspot.com/2010/03/latest-version-of-rcsb-pdb-web-site.html">pre-calculated and systematic protein structure alignment</a>s already for about two years. Every week we run systematic structure alignments for newly released proteins across a representative subset of the database and try to identify related proteins based on their 3D shape. <br />
<br />
This week we have released<a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1203"> a major upgrade</a> to those efforts. Our pre-computed alignments are now using domain information to split protein chains into smaller subunits. We introduced this change because many proteins are built of more than just one domain. In that case our previous results were a bit unclear in the sense that results for any of the domains were displayed together and that made the data more difficult to compare and interpret.<br />
<br />
The new domain based procedure is using the <a href="http://scop.mrc-lmb.cam.ac.uk/">SCOP</a> domain assignments where available to define how to break up protein chains. If the structures are too new to be annotated by SCOP (like all newly released proteins), then we use a software called ProteinDomainParser to define domains based on geometric criteria. Even if the algorithm sometimes defines a break point that might not be the same what SCOP would define, it is still interesting if you find structural neighbors with such fragments of proteins.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.rcsb.org/pdb/general_information/new_images/1203_domBasedSeqImg3BMV.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="67" src="http://www.rcsb.org/pdb/general_information/new_images/1203_domBasedSeqImg3BMV.png" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
In addition, this release of the RCSB PDB web site also provides a new display of protein chains and how different sources annotate protein domains (see the image above). This domain summary shows SCOP domains, ProteinDomainParser domains and Pfam domains. Here an example for <a href="http://www.rcsb.org/pdb/explore/structureCluster.do?structureId=3BMV">a Cyclodextrin glycosyl transferase (3BMV</a>) from Thermoanerobacterium thermosulfurigenes. It is composed of four domains, which are identified by all of the three data sources.<br />
<br />
<br />
<br />Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-32435049975607599442012-04-27T17:01:00.001-07:002012-04-27T17:03:01.150-07:00java.sun.com down?!I just realized that java.sun.com is not reachable and java.net displays this little message:<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgajDxmra8c3Mf3FQS9U-1CG8rCqIGsw_vmz0FtrunJ6QGoQCam9NFxxrmi-gnKpe1azBFzsuQqgO0w1sXUx_8-3EyaWqHDXaXa0YGlPnPlaWRTaRCBTEC7EMGx8z41fs-di63BvII8lVo/s1600/Screen+Shot+2012-04-27+at+16.52.34.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="144" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgajDxmra8c3Mf3FQS9U-1CG8rCqIGsw_vmz0FtrunJ6QGoQCam9NFxxrmi-gnKpe1azBFzsuQqgO0w1sXUx_8-3EyaWqHDXaXa0YGlPnPlaWRTaRCBTEC7EMGx8z41fs-di63BvII8lVo/s320/Screen+Shot+2012-04-27+at+16.52.34.png" width="320" /></a></div>
<br />
<br />
Thanks to google cache (all the sites containing the original info are unreachable as well) I found a notification in one of the Java User groups:<br />
<br />
<br />
<div style="background-color: #ffcccc; border-bottom-color: rgb(255, 0, 0); border-bottom-style: solid; border-bottom-width: 1px; border-image: initial; border-left-color: rgb(255, 0, 0); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(255, 0, 0); border-right-style: solid; border-right-width: 1px; border-top-color: rgb(255, 0, 0); border-top-style: solid; border-top-width: 1px; font-size: 1em; margin-bottom: 0.5em; padding-bottom: 0.5em; padding-left: 0.5em; padding-right: 0.5em; padding-top: 0.5em; text-align: center;">
<span style="color: red;">Notice: Java.net will be offline starting around noon pacific time (7pm UTC) on Friday, April 27, through noon pacific time (7pm UTC) on Monday, April 30 for scheduled maintenance.</span></div>
<div>
<span style="color: red;"><br /></span></div>
<div>
<br /></div>
<div>
A planned downtime of three days. If we would do that at work we would get into serious trouble! We go through all sorts of efforts to ensure 24/7 availability and even if we have major site updates we don't let that impact our availability.</div>
<div>
<br /></div>
<div>
I noticed this because one of my tomcat instances did now want to start up which was caused by a failing XML- dtd validation. </div>
<div>
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXOQASvloY3DDTPx7yCHpcyHIfx81IuZFYgHOahztaAlGKTFRJq5txKbvBtQKbOwnE8UcXAh0e38qDf4VOszU_j7VsVuTfkjMGON2aFpafQPI8noUxlpb3nD9wKQC8nNeOkUxXXC0DxaE/s1600/Screen+Shot+2012-04-27+at+16.54.55.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="193" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXOQASvloY3DDTPx7yCHpcyHIfx81IuZFYgHOahztaAlGKTFRJq5txKbvBtQKbOwnE8UcXAh0e38qDf4VOszU_j7VsVuTfkjMGON2aFpafQPI8noUxlpb3nD9wKQC8nNeOkUxXXC0DxaE/s320/Screen+Shot+2012-04-27+at+16.54.55.png" width="320" /></a></div>
<div>
<br /></div>
<div>
Luckily this can be easily fixed by removing the dtd validation in the xml file. However I wonder how many tomcat servers world wide will have similar problems to start up until Monday! Such a long downtime of such "standard" URLs is rather unprofessional IMHO.</div>
<div>
<br /></div>
<div>
<br /></div>
<div>
<br /></div>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com1tag:blogger.com,1999:blog-120256850987994647.post-50306432178588987732012-04-17T08:09:00.002-07:002012-04-17T08:09:59.483-07:00On Wikipedia's front pageOur article on <a href="http://en.wikipedia.org/wiki/Circular_permutation_in_proteins">Circular permutation in proteins</a> has made it on the <a href="http://en.wikipedia.org/wiki/Main_Page">wikipedia front page</a>!<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJWJ6hXLyA51UaZsCFMLXfKGVfA1JOn9U6Vrh_u5jgE0LUbgBKPHFPKsuMM1lx6I0Tl_D-ZsqvRvFi7utgp8maPZ4YJLeEA0lv01LhyrlMyEqQHI24YbxZ2qeKghsJnNKzT07Of9-2-3I/s1600/Screen+shot+2012-04-17+at+7.48.43+AM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="244" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJWJ6hXLyA51UaZsCFMLXfKGVfA1JOn9U6Vrh_u5jgE0LUbgBKPHFPKsuMM1lx6I0Tl_D-ZsqvRvFi7utgp8maPZ4YJLeEA0lv01LhyrlMyEqQHI24YbxZ2qeKghsJnNKzT07Of9-2-3I/s320/Screen+shot+2012-04-17+at+7.48.43+AM.png" width="320" /></a></div>
<br />Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-58565603487568205972012-03-29T15:40:00.001-07:002012-03-29T17:48:28.144-07:00PLoS comp biol goes Wikipedia<a href="http://wikipedia.org/">Wikipedia</a> has become a primary resource of information for many students when looking up basic information. However there is an interesting gap between the scientific community and the people who are regularly contributing to wikipedia articles. There are only few prominent scientists who are regulars, such as the <a href="http://www.ncbi.nlm.nih.gov/pubmed/22144683?dopt=Abstract">Pfam authors</a> who recently <a href="http://www.ncbi.nlm.nih.gov/pubmed/22127870">integrated wikipedia into the Xfam</a> series of databases. Another major science related project on wikipedia with about ten thousand articles describing various genes is <a href="http://en.wikipedia.org/wiki/Portal:Gene_Wiki">GeneWiki</a>, lead by <a href="http://sulab.org/">Andrew Su</a>. A possible reason for this difference in communities might be the lack of acceptance as academic publishing for wikipedia articles. As of today PLoS comp biol tries to resolve this disparity by publishing a new type of manuscripts, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002446">Topic Pages</a>.<br />
<br />
<i>Topic Pages</i> are designed to provide review style articles. These articles serve as a copy of reference, that can be cited and will show up in <a href="http://www.ncbi.nlm.nih.gov/pubmed/">Pubmed</a>. It will also be released at wikipedia where a living copy of the document can be edited and updated by the wider public. This is done in collaboration with the wikiproject <a href="http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Computational_Biology#PLoS_Computational_Biology_to_Contribute_Wikipedia_pages.3F">computational biology</a>. <br />
<br />
How does this work? In short, an article is first submitted to PLoS where it is peer reviewed and upon acceptance it will be published by PLoS comp biol as well as uploaded to wikipedia. While this sounds rather straightforward, one of the issues with this approach is around licensing.<br />
<br />
PLoS is publishing all articles under a very liberal license, <a href="http://www.ploscompbiol.org/static/license.action">the Creative Commons Attribution License</a>. This means, you can do with the article what you want, even change the license, as long as you credit the original sources. This license is in fact more liberal than the wikipedia license, which is <a href="http://en.wikipedia.org/wiki/Wikipedia:Text_of_Creative_Commons_Attribution-ShareAlike_3.0_Unported_License">Creative Commons Attribution Share Alike</a>. This means we can take a PLoS comp biol article and publish it on wikipedia, as long as we cite the original source of the text, but we can not do this in the opposite direction.<br />
<br />
In order to avoid any licensing conflicts, <a href="http://en.wikipedia.org/wiki/User:Quantum7">Spencer Bliven</a> set up a custom Mediawiki instance with the liberal PLoS style license. It can be found at <a href="http://topicpages.ploscompbiol.org/">http://topicpages.ploscompbiol.org/</a>. By drafting the manuscript there we are able to transfer the content easily over to both PLoS and wikipedia, once it has passed the PLoS review process. Besides this, also the review process is transparent and you can see what the referees commented on our article at the talk page of the article (both at wikipedia and the topicpages sites)<br />
<br />
Our <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002445"> latest paper</a> is the first such <i>Topic Page</i>. It provides a review on<a href="http://en.wikipedia.org/wiki/Circular_permutation_in_proteins"> Circular Permutations in proteins</a>, a type of relationship in proteins, whereby the proteins have a changed order of amino acids in their protein sequence while their 3D shape remains very similar.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://upload.wikimedia.org/wikipedia/commons/5/52/Concanavalin_A_vs_Lectin.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="209" src="http://upload.wikimedia.org/wikipedia/commons/5/52/Concanavalin_A_vs_Lectin.png" width="320" /></a> (<a href="http://upload.wikimedia.org/wikipedia/commons/5/52/Concanavalin_A_vs_Lectin.png">image Wikipedia</a>)</div>
<br />
<br />
For more information read the full <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002445">article at plos</a> ( doi:10.1371/journal.pcbi.1002445 ) or take a look at the <a href="http://en.wikipedia.org/wiki/Circular_permutation_in_proteins">latest version of this at wikipedia.</a> Also read the <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002446">PLoS comp biol editorial</a>, announcing the Topic Pages<br />
<br />
<br />Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-6709300018839860232012-03-18T09:57:00.001-07:002012-03-18T09:57:41.304-07:00GSoC 2012 - how to get started with a proposal<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">To get </span><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">started with a proposal I would recommend to look at the BioJava</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">project proposals from the <a href="http://biojava.org/wiki/Google_Summer_of_Code_2011">last two years</a> (<a href="http://biojava.org/wiki/Google_Summer_of_Code_2010">and here</a>) and</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">see what kind of projects got funded and how those proposals were</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">written. Think about what you would like to work on. Get a copy of</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">BioJava and see how related features are working. Come up with a plan</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">on how to extend this.</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">We are fairly flexible regarding what kind of projects we will run</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">this summer and this really depends on the submitted project</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">proposals. All proposals will be compared and ranked together with</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">other projects from the Bio* projects. As such a good proposal is key</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">to get funded.</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">A good proposals shows</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">- the motivation of the student</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">- that the candidate is qualified to do what he is proposing</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">- adds useful new functionality to BioJava</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">- discusses possible risks and what to do about them</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">It is difficult to answer questions like "how should I perform this or</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">that project?" - There are more than one possible path and it depends</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">on your skills and interest what will be the best answer for this.</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">Overall I recommend to pick a project on a topic that is close to your</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">(future?) thesis, or is of particular interest for you.</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">Here a couple of more thoughts which are project specific:</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">- The best projects are those that you come up with yourself. If you</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">want to distinguish yours from every other proposal, suggest something</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">which is not on our list.</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">- File parsers:</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">if you want to work on file parsers take a look at existing ones. What</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">features do they provide? How can they be extended? For example if you</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">want to work on the CATH parser, take a look at how the SCOP parser</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">works. What features are available around this (access to domains) and</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">how can something like this be set up for CATH. Look at how the CATH</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">website provides files.</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">- Porting of algorithms:</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">There are several approaches possible for doing this. I recommend that</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">you should have some background both in C and in Java for this. Get a</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">copy of the algorithm you want to port, compile it, and take a look at</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">the source. There are several ways how to proceed for the actual port</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">and having a good strategy for this is key for this proposal. Perhaps</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">try to use your strategy on some simple test case to see how this</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">might work.</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">- BioJava in the cloud</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">The goal here is parallelization of existing code. What parts of</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">biojava are suitable for this? How can they be parallelized and moved</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">to current cloud infrastructure? There is a lot of online material</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">available for this which will be helpful here.</span>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-76769136333961449252012-03-16T18:50:00.001-07:002012-03-16T18:50:51.608-07:00BioJava at at Google Summer of Code 2012<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">The Open Bioinformatics foundation as an umbrella organisation for</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">BioJava has been accepted to participate in this year's Google Summer</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">of Code. </span><br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.google-melange.com/soc/content/2-0-20120316-p1/images/v2/gsoc/logo/banner-gsoc2012.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="66" src="http://www.google-melange.com/soc/content/2-0-20120316-p1/images/v2/gsoc/logo/banner-gsoc2012.png" width="400" /></a></div>
<br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">This means we will again be able to offer mentoring through BioJava</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">this year. Accepted students will get a stipend of 5,000$ from Google.</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">Participation is possible from most countries in the world, as long as</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">you are eligible to work in the country in which you'll reside</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">throughout the duration of the program.</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">If you are interested in working on a BioJava related project, now is</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">the time to start preparing and discussing your proposals. For the</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">last two years we had many applications for the projects proposed by</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">mentors. If you want to distinguish your application I recommend to</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">propose your own project. Don't forget to discuss any proposal with</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">us before you submit them. We will try to provide feedback and match</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">you with a suitable Mentor.</span><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">Also see </span><a href="http://biojava.org/wiki/Google_Summer_of_Code" style="background-color: rgba(255, 255, 255, 0.917969); color: #1155cc; font-family: arial, sans-serif; font-size: 13px;" target="_blank">http://biojava.org/wiki/<wbr></wbr>Google_Summer_of_Code</a><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;"> and Google's</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">FAQs: </span><a href="http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs" style="background-color: rgba(255, 255, 255, 0.917969); color: #1155cc; font-family: arial, sans-serif; font-size: 13px;" target="_blank">http://www.google-melange.com/<wbr></wbr>document/show/gsoc_program/<wbr></wbr>google/gsoc2012/faqs</a><br />
<br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">The student application deadline is April 6th. Google will announce</span><br />
<span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;">which proposals got accepted on April 23rd.</span><br />
<span style="color: #222222; font-family: arial, sans-serif; font-size: x-small;"><br /></span>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-32619079762578738712012-03-16T18:45:00.000-07:002012-03-16T18:45:44.740-07:00BioJava 3.0.3 released<span style="font-family: inherit;"><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">BioJava 3.0.3 has been released and is available from</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><a href="http://www.biojava.org/wiki/BioJava:Download" style="background-color: rgba(255, 255, 255, 0.917969); color: #1155cc;" target="_blank">http://www.biojava.org/wiki/<wbr></wbr>BioJava:Download</a><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;"> as well as from the</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">BioJava maven repository at </span><a href="http://www.biojava.org/download/maven/" style="background-color: rgba(255, 255, 255, 0.917969); color: #1155cc;" target="_blank">http://www.biojava.org/<wbr></wbr>download/maven/</a><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;"> .</span></span><br />
<span style="font-family: Times, 'Times New Roman', serif; font-size: large;"><br /></span><br />
<span style="font-family: Times, 'Times New Roman', serif; font-size: large;">New Features</span><br />
<span style="font-family: inherit;"><br style="background-color: rgba(255, 255, 255, 0.917969);" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">BioJava 3.0.3 adds several new features</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">- Significant improvements for the web service module (ncbi blast and</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">hmmer web services)</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">- Fastq parser (ported from the biojava 1 series to version 3)</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">- Support for SIFTS-PDB to UniProt mapping</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">- Improved support for working with external protein domain definitions</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">- Protmod module renamed to modfinder</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">- Numerous improvements all over the place (several hundred commits</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">since last release)</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">- We are also working on an update for the legacy biojava 1.8 series.</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">This release would not have been possible with contributions from</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">numerous people, thanks to all for their support!</span><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><br style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;" /><span style="background-color: rgba(255, 255, 255, 0.917969); color: #222222;">Happy BioJava-ing!</span></span><span style="color: #222222; font-family: arial, sans-serif; font-size: x-small;"><br /></span>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-75477757479062052372011-12-10T16:21:00.001-08:002011-12-10T17:00:56.721-08:00RCSB PDB Fall 2011 web site update<a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1111">Another major website update has been released</a> for the RCSB web site. One of the main new features is Peter's new visualisation of surfaces with the Protein Workshop viewer. The calculation of surfaces is extremely fast and the resulting images look amazing. Here the capsid of a rather large virus (PBCV-1) - PDB ID <a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=1M4X">1M4X</a>.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGpMKj186tX13XZdox617ffyDZSp_4cP1opZ2vcTd7Jed3Tdh9fzEb9bJGXEAs_Ca3WJv0gNsiTVFyNONdwZ2drLDETXE5f5vCDBUhnCZMy79D1GCuitoBoy71TbLzyu2IwiqxoK7AwOQ/s1600/Screen+shot+2011-12-10+at+4.38.18+PM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="281" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGpMKj186tX13XZdox617ffyDZSp_4cP1opZ2vcTd7Jed3Tdh9fzEb9bJGXEAs_Ca3WJv0gNsiTVFyNONdwZ2drLDETXE5f5vCDBUhnCZMy79D1GCuitoBoy71TbLzyu2IwiqxoK7AwOQ/s320/Screen+shot+2011-12-10+at+4.38.18+PM.png" width="320" /></a></div>
<br />
To visualize the surfaces, simply <a href="http://www.rcsb.org/pdb/explore/viewerLaunch.do?viewerType=PW&structureId=1XI4&unit=bio&unit_id=1">launch Protein Workshop</a> from the viewer menu on the <a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1111#B1111_vis_surfaces">Structure Summary page</a>.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjD5QumvRAKR98SnhPKbQbgrjBVSD6MVpmD07Q39mYh-baFzQi3_q13cFFPqj0hNrslw2INc09rYg08Fdtjvqr5ruTQOxtg1E1-rq2CEy2xIGMhlAO7WC9WspO6jRfKNQ5YCEuNjb1tKyQ/s1600/Screen+shot+2011-12-10+at+4.42.38+PM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjD5QumvRAKR98SnhPKbQbgrjBVSD6MVpmD07Q39mYh-baFzQi3_q13cFFPqj0hNrslw2INc09rYg08Fdtjvqr5ruTQOxtg1E1-rq2CEy2xIGMhlAO7WC9WspO6jRfKNQ5YCEuNjb1tKyQ/s320/Screen+shot+2011-12-10+at+4.42.38+PM.png" width="248" /></a></div>
<br />
<br />
Once the viewer has downloaded and installed itself, turn the surface on by dragging the <i>Surfaces </i>handle from <i>Off</i> to <i>Opaque. </i><br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDj774vyBAQn6Kv0ULS3dcFw9xd6dO9EpZIGKLRcso4rz0OWqIsrI0z1RL6MYc-DGG5fs1Jny_hrMdXzNUvLnKd-Aitb8wYpiNCcm3mzVabBWuS2nWNRkg3HfusCpQNiSP_VGuIjvTyuQ/s1600/Screen+shot+2011-12-10+at+4.38.37+PM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="119" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDj774vyBAQn6Kv0ULS3dcFw9xd6dO9EpZIGKLRcso4rz0OWqIsrI0z1RL6MYc-DGG5fs1Jny_hrMdXzNUvLnKd-Aitb8wYpiNCcm3mzVabBWuS2nWNRkg3HfusCpQNiSP_VGuIjvTyuQ/s320/Screen+shot+2011-12-10+at+4.38.37+PM.png" width="320" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
There are quite a number of display options, for a more detailed descriptions of all display options <a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1111#B1111_vis_surfaces">view here</a>. </div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.rcsb.org/pdb/general_information/new_images/1111_2rh1_hydro_large.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em; text-align: left;"><img border="0" height="150" src="http://www.rcsb.org/pdb/general_information/new_images/1111_2rh1_hydro_large.png" width="200" /></a><a href="http://www.rcsb.org/pdb/general_information/new_images/1111_1e79_color_large.png" imageanchor="1" style="clear: right; display: inline !important; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img border="0" height="150" src="http://www.rcsb.org/pdb/general_information/new_images/1111_1e79_color_large.png" width="200" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<br />
A list of all the new features of the Fall 2011 release, is available on the <a href="http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1111">"what's new page"</a>.<br />
<i><br /></i>Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com0tag:blogger.com,1999:blog-120256850987994647.post-44398017335070451272011-11-19T10:06:00.001-08:002011-11-19T12:19:04.034-08:00Google Scholar Citations Open To AllThis week <a href="http://scholar.google.com/">Google Scholar</a> citations <a href="http://googlescholar.blogspot.com/2011/11/google-scholar-citations-open-to-all.html">opened up to the public</a>. After the <a href="http://openbioinformatics.blogspot.com/2011/07/google-scholar-citations-google-scholar.html">initial release</a> which was providing limited access only, the latest versions is now open for all scientists. What is interesting is that they seem to have created profiles for many scientists in an automated way. While the transparency of this is amazing, I can also imagine that there will be a push-back about privacy issues.<br />
<br />
You can check out e.g who are the <a href="http://scholar.google.com/citations?view_op=search_authors&hl=en&mauthors=label:computational_biology">most cited scientists in Computational Biology</a> or <a href="http://scholar.google.com/citations?hl=en&view_op=search_authors&mauthors=ucsd">scientists at UCSD</a> or check out Author profiles (e.g. <a href="http://scholar.google.com/citations?user=LnXh0T8AAAAJ&hl=en">yours truly</a>). At the moment those lists are sorted by number of citations. Would be nice to have a few more sort fields like the already calculated h-index. Another missing feature is an API. Would be nice to be able to script their database and create custom reports.<br />
<br />
I believe Google Scholar is setting a new standard for tracking success of scientists and is a serious threat to the ISI web of knowledge.<br />
<br />
<br />Ahttp://www.blogger.com/profile/14312808974629818240noreply@blogger.com1