[3dem] PDBe Workshop: Programmatic Access to Macromolecular Structure Information

[Ardan Patwardhan]

Dear all

PDBe recently introduced an API to provide programmatic access to PDB and EMDB data. Below are details on a workshop we are organising on using the API.

Best wishes

Ardan Patwardhan
Coordinator - cellular structure & PDBe production
Protein Data Bank in Europe (PDBe)
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Tel: +44 1223 492649

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Programmatic Access to Macromolecular Structure Information

PDBe Workshop for Programmers, 24-25 September 2015

Deadline for application: Friday 26 June 2015

==== What?
The Protein Data Bank in Europe (PDBe; www.ebi.ac.uk/pdbe/) is organising a hands-on, interactive workshop for developers interested in using primary and value-added information about the 3D structures in PDB and EMDB. Programmatic access to macromolecular structure data as well as information about assemblies, structure quality, literature and citations, and up-to-date cross-references to other biomedical resources (UniProt, Pfam, CATH, SCOP, etc.) are a critical requirement for integrative bioinformatics analyses and workflows.
PDBe has developed a set of REST APIs (http://www.ebi.ac.uk/pdbe/api/doc) that provide easy access to high-quality information regarding biomacromolecular structures archived in PDB and EMDB. They provide a simple, reliable, light-weight mechanism to query macromolecular structure data, select entries or molecules of interest, and access targeted information about them, including information about the molecules, experimental details, assemblies, motifs, function, taxonomy, structure quality, etc. The API is used by PDBe services and is also integrated in Jmol/JSmol. We will also present Solr/Lucene based query API for macromolecular structure information including PDB, EMDB and value added information on assemblies, structure quality and up-to-date cross-reference information to other biomedical databases based on SIFTS (http://pdbe.org/sifts) .

==== Is it for me?
Do you (plan to) develop software or online resources that use or need access to information about structures in PDB or EMDB? Would you rather not maintain your private infrastructure for retrieving, parsing, storing and updating such information?
If so, then this workshop is for you. We will explain what information is available through the API and how you can access it from your own software or resource. There will be plenty of time for hands-on work where experienced PDBe developers will help you to use the API for your specific needs.

==== When and where?
The workshop will take place on 24 & 25 September 2015 (starting at 12.00 on 24 September, and finishing at 16.00 on 25 September) at EMBL-EBI (www.ebi.ac.uk) in Hinxton, near Cambridge.

==== How much does it cost?
There is no fee for the workshop. However, we expect you to arrange and pay for your own travel to and from EMBL-EBI.
Accommodation will be provided if required at the Wellcome Trust Conference Centre www.wtconference.org.uk which is on the same campus as EMBL-EBI.
Refreshments, lunch on both days and a workshop dinner on 24 September will all be provided.

==== How can I apply?
To apply for the workshop, email Jose Dana at dana at ebi.ac.uk no later than Friday 26 June with the following details:
a brief description of the software you have developed or are developing - i.e. what it does, in which field, how many users, relevant publications, etc.
programming language(s) you are specifically interested in (Python examples and tutorials will be provided)
how you would benefit from this workshop
any specific topics or questions you would like to see addressed in the workshop
If the workshop is oversubscribed, we will select participants based on the information provided.
You will be informed by the end of June if you have been selected for the workshop or not.

==== Prerequisites?
Basic programming experience in use of REST API’s. Bring your own laptop with git and iPython notebook pre-installed if you want to follow the Python tutorial and examples. If you need to make plots, make sure that matplotlib is also installed.

===== Questions?
Jose Dana (dana at ebi.ac.uk) at PDBe will be happy to answer any queries you have about the workshop.
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