The two main goals of this virtual hackathon are:
To develop open source software modules and collaboration tools for universal biomolecular analyses enabling integration of diverse knowledge and datasets.
To create a sustainable diverse community of developers and designers for continued development of such tools.
During last year Hackathon at ISMB2020, we started a series of developments towards the in-depth and systematic analysis of molecular interactions, applied in particular to SARS-CoV-2 proteins and their cell surface receptor. We also took some initial steps in the area of annotations of topological domains of membrane protein receptors, and we opened up iCn3D to evolve towards an open platform to interoperate with external data and software. A feature unique to iCn3D is the ability to share data analysis and structural views through a simple web link (example).
Since then, some of the tools prototyped during the hackathon were productized by NCBI:
We consolidated the link sharing mechanism to enable collaborative research and publication of 3D visualizations, making by the same token iCn3D a platform to make data FAIR: Findable, Accessible, Interoperable, and Reusable, and to go even further in making the computational analyses that operate on the data and produce further data and annotations Reproducible, a process we can call FAIR+R or FAIRR .
We consolidated the molecular interactions analysis in 2D and 3D.
Naturally, new ideas of further developments also emerged as a follow up and considering the evolution during the pandemic of the sheer amount of scientific data produced, and the need to make structural information accessible and “actionable”, in particular to scientists with little knowledge in structure has emerged with an acuity never seen before.
On (1), the means to handle large amounts of data, our initial effort is focused on sequence-structure data, yet it will have to evolve towards a diversity of data relating to sequence, structure, and function. (2) is a much bigger challenge than making data and analyses FAIRR, and we believe that extending 2D visualization is a path to address this challenge. It is not exactly new, we had already initiated some developments during the ISMB2016 hackathon and a few elements were prototyped, however developing universal software in that vein requires innovation both conceptually and algorithmically. These aspects are the motivation behind the project themes listed below.
We propose a list of potential projects spanning six themes listed below, where each team will have a leader along with 2-5 additional developers and a subject-matter expert interested in the topic. Anyone with passion and knowledge interested in leading a project that fits one of the themes below can propose a project by filling out the Project Pitch form or by contacting Ravi Abrol (abrol@csun.edu), if he/she can recruit among registered participants and/or invite new participants.
1. ANALYSIS OF BIOMOLECULAR INTERACTIONS AND MUTATIONS
2. ANALYSIS OF BIOMOLECULAR FLEXIBILITY AND SYMMETRY
3. BIOMOLECULAR REPRESENTATIONS AND VISUALIZATION
4. ANALYSIS OF LARGE DATASETS
5. DATABASES AND ANNOTATIONS
6. COLLABORATION INTERFACES AND DATA SHARING MECHANISMS
To register for the hackathon, please complete this application form.
Applications are due 23 July 2021 by 9pm UTC.
There is no registration fee for the Hackathon@ISMB2021 beyond your normal ISMB2021 registration fees. You have to be registered at ISMB2021 to participate in this hackathon.
A team will be composed of individuals who all have different backgrounds and skills. We know by experience that blending a diverse set of skills is what forms a good team. We are welcoming hard core programmers as well scientists with little programming experience, as long as they have knowledge on the scientific application side. Some participants may have both sides and some may have one side, but the outcome of any project is a team effort.
We encourage researchers working in all areas of computational biology to join us in developing the above mentioned tools. In terms of coding, we will mainly use Python or JavaScript to write code. But any coding experience such as C/C++, JAVA, Perl, Julia, Rust, etc. and/or working knowledge of MySQL, XML, JSON formats should be good enough, especially for algorithmic or database/backend or middleware development. Experience with deployment of web-based tools will also be very useful. Our code will be deposited into GitHub. Some experience in Git/GitHub is helpful. What matters most is to bring new ideas and develop prototype functionality, not a final product. We are also seeking wet lab researchers working on all aspects of protein sequence, structure, and function with to join the hackathon teams to provide scientific input from the point of view of the needs of the community.
Participants will contribute to prototype new open source software functionality, learn new skills, and get a chance to become part of a growing community. One of the objectives of this hackathon is to develop tools and publish their development and/or application as a peer-reviewed publication in the Frontiers in Genetics journal within 3-6 months after the hackathon. Your contributions will be recognized through co-authorship in the submitted manuscripts. In addition, we would like to sustain this community of developers in between the hackathons through dedicated communication channels, as our hope is that you will continue to help develop these tools.
PROGRAM:
a. iCn3D publications: You can familiarize yourself with iCn3D through our recent publication and preprint.
c. iCn3D@GitHub
TUTORIALS and DOCUMENTATION
a. iCn3D Tutorial Part 1 (the basics): Video, Slides
b. iCn3D Tutorial Part 2 (molecular interactions, structural comparisons, etc): Video, Slides
c. Full documentation (Help pages)
Each team will have a Slack subchannel for communication with each other and with the team leader. Each participant will also be part of a Technical Support subchannel, which should be used for technical questions related to github, slack, compute nodes, etc. and which will be monitored continuously by the hackathon’s tech-support team.
We look forward to seeing you at the hackathon!
- Ravi, Philippe, Allissa, Jiyao, Raul