Sequence-Structure Moonlight Hackathon
New Times and Extended Deadlines!

July 8 - 11, 2016
Room: "Asia 3"

In the evenings of July 8th to of July 10th (after regular programming - nightly schedule), NCBI and RCSB PDB will assist ISCB in hosting a sequence-structure hackathon focused on integrating protein structure information and viewers with genomic sequence and variants, pharmacogenomic binding, and improve web based tools to visualize, annotate and share sequence and structure information. 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. The event is open to anyone selected for the hackathon, and registered for the ISMB 2016 meeting. Those coming for the SIGs only can also join the hackathon for a nominal fee of $100 for ISCB members and $150 for nonmembers. For those who want to code all day and night the hackathon rooms will be open around the clock.

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*.

Please see the application for specific team projects.

* Some of the projects will build on existing APIs feeding data to or extracting data from viewers, so not all applicants need a working knowledge of 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, http://mmtf.rcsb.org) for ultrafast access, parsing, and processing of PDB structures.

Organization

After a brief organizational session, teams will spend three evenings 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 (github.com/NCBI-Hackathons). 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 10th, 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 re-apply. The first round of accepted applicants will be notified on June 13th by noon ET, and have until June 15th 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 for regular ISMB meeting attendees, the hackathon sessions will be in the evening as seen in the nightly schedule. Please include a regularly used 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 evenings of the event. A small number of travel awards are available for the hackathon and the meeting. Awards for things like most prolific code development will be given at the ISCB awards ceremony on Tuesday!

For ISMB meeting attendees not participating to SIG meetings, please note that you will need to arrive on Saturday for the first Hackathon evening.

Please contact This email address is being protected from spambots. You need JavaScript enabled to view it. with any questions

Travel Fellowships

Travel funding is available for students and post docs. Funds are limited and will be distributed based on need. Selected participants will receive instructions on how to apply for travel fellowships in June. Travel funding awards will not cover the entire participant’s cost – maximum of $500 per award.