The two main goals of this virtual hackathon are:
To develop open source software modules for universal biomolecular interactions analyses with focus on SARS-CoV-2 and other virus proteins.
To create a sustainable community of developers and designers for continued development of such tools.
Four years ago NCBI started developing iCn3D, a web based software to visualize and analyze molecular structures in 1D/2D/3D (Wang et al. 2020). The collaboration was extended to NCI to tackle immunotherapeutic protein design. The software is open source to invite a community of developers to add modules. We had our first Moonlight hackathon at ISMB 2016 in Orlando that led to an initial 2D visualization functionality as part of a number of projects. Recently, we started a second phase of development towards more in-depth analysis of molecular interactions. With the COVID-19 pandemic, we realized that some of the capabilities for sharing structures and structural analyses with peers, in preprints through URLs could be a valuable mechanism to enable collaborative research between scientists. We are racing to add functionality to broaden analytical capabilities to analyze membrane proteins, cell surface proteins, and to bridge the worlds of sequencing, structure, and function. We also need to make structural information accessible to scientists with little knowledge in structure. The software has integrated the visualization of sequence (1D) and structure (3D) and started on 2D, initially at the ISMB 2016 hackathon. We propose to prototype new functionality on that same hackathon model, this time online at ISMB2020.
There is no registration fee for the hackathon@ISMB beyond your normal ISMB2020 registration fees.
We encourage researchers working in all areas of computational biology to join us in developing the above mentioned analysis tools. In terms of coding, we will mainly use JavaScript or Python to write code. But any coding experience such as C/C++, JAVA, Perl, Julia, etc. and working knowledge of XML and JSON formats should be good enough, especially for algorithmic or database/backend or middleware development. 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 an interest in viral proteins 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 apply these tools to COVID-19 and related proteins. Some of the completed tools and viral applications are expected to result in publications, where your contribution will be recognized through co-authorships. We plan to organize such hackathons every 6 months, with every other hackathon being at ISMB. In addition, we would like to sustain this community of developers in between the hackathons through a dedicated communication channel on Slack, as our hope is that you will continue to help develop these tools.
To register for the hackathon, please complete this application form. Applications are due 11 July 2020 by 4pm EDT.
Participants contribute to prototype new open source software functionality and become part of a community. An effort during the hackathon can lead to productized software. That should be an aim in addition to applying and learning new skills. Since we have an aim not only in coding but in getting concrete results for application, we would like to aim a co-authored publication on the analysis of some of COVID-19 related structure(s) with participants as co-authors. Depending on results, it could be either on Methods, software demonstrating structure based collaborative research, and analysis of protein structure and molecular interactions.
We propose a list of potential projects, 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 contacting Ravi Abrol, if he/she can recruit among registered participants and/or invite new participants.
Theme 1: Using Open Source Platform iCn3D, develop new universal modules for molecular interactions analysis
Differential analysis of viral protein sequence-variants interactions with host proteins
1D/2D/3D MAPS of Viral Surface Protein Domains and Interactions (Intermolecular vs intramolecular)
Integration of externally computed DATA (atom/residue based properties) for visualization on structure and data analysis in a structural context
Adding protein-ligand interactions descriptors useful for structure-based drug discovery
Theme 2: Development of (prototype) Algorithms/Tools/Databases for protein structure and interaction analysis
Creation of a prototype SARS-CoV-2 Virus Mutation Database
Impact of viral protein sequence variants on protein domains and interfaces: Tool to evaluate impact of a mutation
Symmetry, Structural Analysis and Model building
Creation of a Membrane Protein Extended Topology Standard for Surface Proteins
Theme 3: Usability - User Interface, Automation, etc.
Windowing, Data management, Project management, Cloud etc.
Reference sequence numbering and mapping
APPLICATION:
a. Preprint
You can familiarize yourself with iCn3D through our recent preprint. All links show you examples of analyses:"Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19", Youkharibache, Cachau, Madej, Wang (2020) https://www.biorxiv.org/content/10.1101/2020.07.01.182964v2.
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