[phenixbb] PDBe workshop on programmatic access to macromolecular structure information, 20-21 Nov 2014, Cambridge UK

swanand at ebi.ac.uk swanand at ebi.ac.uk
Sun Oct 5 11:42:26 PDT 2014

Programmatic Access to the Macromolecular Structure Information
-------- PDBe Workshop for Programmers, 20-21 Nov 2014 --------

============= What?

The Protein Data bank in Europe (PDBe; http://pdbe.org) 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.) is a critical requirement for
integrative bioinformatics analyses and workflows.

PDBe has developed a set of REST APIs
(http://wwwdev.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
the 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 infromation to other biomedical databases based
on SIFTS (http://pdbe.org/sifts) .

============= Is it for me?

Do you (plan to) develop software or on-line 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!  In the workshop, we will
explain what information is available through the API and how
you can access it from your own software or resource. There is
plenty of time for hands-on work where experienced PDBe
developers will try to help you use the API for your specific

============= When?

20 & 21 November 2014.

============= Where?

EMBL-EBI (http://www.ebi.ac.uk) , Cambridge.

============= How much does it cost?

We expect you to pay for (and arrange) your own travel to and
from Cambridge.  However, there is no fee for the workshop, and
we will provide free accommodation (Holiday Inn Express;
http://www.hiexpresscambridgeduxford.co.uk), transportation
between the hotel and the EMBL-EBI, coffee/tea, lunches and a
workshop dinner on the 20th. This is all thanks to generous
funding from the Wellcome Trust to PDBe.

============= How can I apply?

E-mail Swanand Gore (swanand at ebi.ac.uk) or Jose Dana
(dana at ebi.ac.uk) at PDBe no later than 20 October 2014 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 October if you have been
selected or not, or whether you are on the stand-by list.

============= 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?

Swanand Gore (swanand at ebi.ac.uk) or Jose Dana (dana at ebi.ac.uk)
at PDBe will be happy to answer your queries.
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