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/
<http://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 <http://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 Centrewww.wtconference.org.uk
<http://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 d...@ebi.ac.ukno later
than Friday 26 Junewith 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 (d...@ebi.ac.uk) at PDBe will be happy to answer any queries
you have about the workshop.
