News
Join the Sequence-Structure Hackathon at ISMB Orlando 2016
05/24
From the evening of July 8th to the morning of July 11th, NCBI and the RCSB PDB will assist the International Society for Computational Biology (ISCB) in hosting a sequence-structure hackathon focused on integrating protein structure information and viewers with genomic sequence and variants, pharmacogenomic binding, and general laboratory practice. To apply for this hackathon, complete this form (approximately 10 minutes to complete). Applications are due June 10th, 2016 by 5 pm ET.
This event is for students, postdocs and investigators or other researchers already engaged in the use of JavaScript-based viewers for protein structure visualization and/or genome/gene/protein sequence browsers. It is open to anyone selected for the hackathon, and registered for the ISMB 2016 meeting.
Working groups of 5-6 individuals will be formed into five or six teams. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. The potential subjects for this iteration are:
- Presenting data to and from JavaScript-viewable protein structures,
- Simplified structure diagrams,
- A digital notebook for structural biologists,
- And pharmacogenomic association in conserved binding sites*.
* Some of the projects will build on APIs feeding data to or extracting data from viewers, so applicants need not be working on JavaScript viewers per se. For example, there is an opportunity to interface existing applications and libraries using any programming language with the Macromolecule Transmission Format (MMTF) for ultrafast access, parsing, and processing of PDB structures.
Please see the application for specific team projects.
Organization
After a brief organizational session, teams will spend three days analyzing a challenging set of scientific problems related to a group of datasets. Participants will analyze and combine datasets in order to work on these problems.
Datasets
Datasets will come from the public repositories housed at the NCBI, PDB and elsewhere.
Products
All pipelines and other scripts, software and programs generated in this course will be added to a public GitHub repository designed for that purpose. A manuscript outlining the design and usage of the software tools constructed by each team will be submitted to an appropriate journal.
Application
To apply, complete this form (approximately 10 minutes to complete). Applications are due June 1st, 2016 by 5 pm ET. Participants will be selected from a pool of applicants based on the experience and motivation they provide on the form. Prior participants and applicants are especially encouraged to reapply. The first round of accepted applicants will be notified on June 3rd by 5 pm ET, and have until June 6th at noon to confirm their participation.
If you confirm, please make sure it is highly likely you can attend, as confirming and not attending bars other data scientists from attending this event. We understand this hackathon is going on during an information-dense scientific meeting, so we ask that attendees attend at least part of three out of five scientific sessions in the draft daily schedule. Please include a monitored email address, in case there are follow-up questions.
Note: Participants will need to bring their own laptop to this program. A working knowledge of scripting (e.g., Shell, Python) is necessary to be successful in this event. Knowledge of JavaScript will be particularly helpful in this event. Applicants must be willing to commit to all three days of the event. No financial support for travel, lodging or meals is available for this event. Also note that the event may extend into the evening hours on Friday and/or Saturday. Please make any necessary arrangements to accommodate this possibility. Awards for achievements like "Most Prolific Code Development" will be given at the ISCB awards ceremony on Tuesday.
Please contact [email protected] with any questions.
