<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>===============================================================</div>Programmatic Access to the Macromolecular Structure Information<br>===============================================================<br>-------- PDBe Workshop for Programmers, 20-21 Nov 2014 --------<br><br><br>============= What?<br><br><br>The Protein Data bank in Europe (PDBe;<a href="http://pdbe.org">http://pdbe.org</a>) is<br>organising a hands-on, interactive workshop for developers<br>interested in using primary and value-added information about<br>the 3D structures in PDB and EMDB. Programmatic access to<br>macromolecular structure data as well as information about<br>assemblies, structure quality, literature and citations,<br>and up-to-date cross-references to other biomedical resources<br>(UniProt, Pfam, CATH, SCOP, etc.) is a critical requirement for<br>integrative bioinformatics analyses and workflows.<br><br>PDBe has developed a set of REST APIs<br>(<a href="http://wwwdev.ebi.ac.uk/pdbe/api/doc">http://wwwdev.ebi.ac.uk/pdbe/api/doc</a>) that provide easy access<br>to high-quality information regarding biomacromolecular<br>structures archived in PDB and EMDB. They provide a simple,<br>reliable, light-weight mechanism to query macromolecular<br>structure data, select entries or molecules of interest, and<br>access targeted information about them, including information<br>about the molecules, experimental details, assemblies, motifs,<br>function, taxonomy, structure quality, etc. The API is used by<br>the PDBe services and is also integrated in Jmol/Jsmol. We will<br>also present Solr/Lucene based query API for macromolecular<br>structure information including PDB, EMDB and value added<br>information on assemblies, structure quality and up-to-date<br>cross-reference infromation to other biomedical databases based<br>on SIFTS (<a href="http://pdbe.org/sifts">http://pdbe.org/sifts</a>) .<br><br><br>============= Is it for me?<br><br><br>Do you (plan to) develop software or on-line resources that use<br>or need access to information about structures in PDB or EMDB?<br>Would you rather not maintain your private infrastructure for<br>retrieving, parsing, storing and updating such information?<br><br>If so, then this workshop is for you! In the workshop, we will<br>explain what information is available through the API and how<br>you can access it from your own software or resource. There is<br>plenty of time for hands-on work where experienced PDBe<br>developers will try to help you use the API for your specific<br>needs.<br><br>============= When?<br><br><br>20 & 21 November 2014.<br><br><br>============= Where?<br><br><br>EMBL-EBI (<a href="http://www.ebi.ac.uk">http://www.ebi.ac.uk</a>) , Cambridge.<br><br><br>============= How much does it cost?<br><br><br>We expect you to pay for (and arrange) your own travel to and<br>from Cambridge. However, there is no fee for the workshop, and<br>we will provide free accommodation (Holiday Inn Express;<br><a href="http://www.hiexpresscambridgeduxford.co.uk">http://www.hiexpresscambridgeduxford.co.uk</a>), transportation<br>between the hotel and the EMBL-EBI, coffee/tea, lunches and a<br>workshop dinner on the 20th. This is all thanks to generous<br>funding from the Wellcome Trust to PDBe.<br><br><br>============= How can I apply?<br><br><br>E-mail Swanand Gore (<a href="mailto:swanand@ebi.ac.uk">swanand@ebi.ac.uk</a>) or Jose Dana<br>(<a href="mailto:dana@ebi.ac.uk">dana@ebi.ac.uk</a>) at PDBe no later than 20 October 2014 with the<br>following details:<br>* a brief description of the software you have developed or are<br>developing - i.e. what it does, in which field, how many users,<br>relevant publications, etc.<br>* programming language(s) you are specifically interested in<br>(python examples and tutorials will be provided).<br>* how you would benefit from this workshop.<br>* any specific topics or questions you would like to see<br>addressed in the workshop.<br><br>If the workshop is oversubscribed, we will select participants<br>based on the information provided.<br><br>You will be informed by the end of October if you have been<br>selected or not, or whether you are on the stand-by list.<br><br><br>============= Prerequisites?<br><br><br>Basic programming experience in use of REST API’s. Bring your<br>own laptop with git and iPython notebook pre-installed if you<br>want to follow the python tutorial and examples. If you need to<br>make plots, make sure that matplotlib is also installed.<br><br><br>============= Questions?<br><br><br>Swanand Gore (<a href="mailto:swanand@ebi.ac.uk">swanand@ebi.ac.uk</a>) or Jose Dana (<a href="mailto:dana@ebi.ac.uk">dana@ebi.ac.uk</a>)<br>at PDBe will be happy to answer your queries.<div><br></div><div></div></body></html>