Award Winners

Ian Lawson Van Toch Memorial Award for Outstanding Student Paper
RCSB PDB Poster Prize
Special Session: Representation learning in biology
Special Session: Emerging gain-of-function mutations and multi-omics network biology
Bio-Ontologies COSI – Best Talk Award
Bio-Ontologies COSI – Best Poster Award
BioVis COSI – Best Abstract
BioVis COSI – Test-of-Time Award
CAMDA COSI – Best Talk Awards
CAMDA COSI – Best Poster Award
CompMS COSI – Best Talk Award
CompMS COSI – Best Poster Award
EvolCompGen COSI - Best Talk Award
EvolCompGen COSI - Best Poster Award
iRNA COSI – Best Poster Award
NetBio COSI – Best Talk Award
NetBio COSI – Best Poster Award
SysMod COSI - Best Poster Awards
TransMed COSI Best Oral Presentation Awards
TransMed COSI Best Poster Awards

Download Closing Slides

With Support From:

Tsukasa Nakamura, JSPS(PD)/Tohoku University
Towards protein interface prediction using SE(3)-Transformer

ISMB/ECCB 2021

More than 2,100 participants from nearly 80 countries joined us for ISMB/ECCB 2021.  We hope you enjoyed your experience. Registrants of the conference will continue to have exclusive access to the platform until Nov. 30. After which, all content for which ISCB has received permission will move to ISCBtv.

Thank you for attending ISMB/ECCB 2021!

We hope to see you in Madison, USA for ISMB 2022, July 10-14, 2022 or
in Sitges, Barcelona, Spain for ECCB 2022, September 18-21, 2022.

Helpful Post Conference Links

ISMB/ECCB 2021 Award Winners
Daily Recaps (Sunday, Monday, Tuesday, Wednesday, Thursday, Friday)
ISCBshowcase, your all bioinformatics emporium
Conference Presentation Permissions Form
Conference Recordings

ISCB Summer Newsletter & Special Issue of Bioinformatics Featuring ISMB/ECCB 2021

Explore the Scientific Program

Information on webinar chat click here

Virtual Conference Optimal Conditions

For the best experience please consider the following in preparation of the conference:

• Ensure you have the latest version of Zoom installed
• Refresh your computer - simply by doing a restart
• Preferred browsers are Chrome and Firefox
• Hardwire your computer vs wifi
• Turnoff other browsers, background programs and eliminate other internet devices being used if possible

Requirements per device and their recommendation for speeds (including Linux, Mac and Microsoft computer requirements for zoom) can be found here

Moderator Resources

Moderator Training: July 13
Moderator Training: July 14

Moderator Tips

Speaker Resources

Speaker Training: July 14
Speaker Training: July 15
Speaker Training: July 19

Zoom backgrounds

SCS Wikipedia Hackathon 2021: Connecting COSIs to Wikipedia

July 23, 2021 at 16:00 - 18:00 UTC

Hackathon RegistrationCheck your local time

The main goals of this hackathon are:

• To better connect ISCB Communities of Special Interest (COSIs) to relevant Wikipedia articles by conducting a wide scale review of current computational biology/bioinformatics-related articles.
• To foster a community of editors with an interest in improving coverage of computational biology topics on Wikipedia.

Background

Open access to scientific information is a core principle of the ISCB. This is a principle shared by the Wikimedia Foundation, with its primary goal to collect, develop and disseminate free and open-access educational content. Consequently, ISCB has and continues to foster strong links with several Wikimedia projects, particularly Wikipedia. The Computational Biology taskforce of WikiProject Molecular Biology has existed in some form since 2007 and is a group of editors overseeing over 1,500 Wikipedia articles relating to computational biology and bioinformatics. Throughout its history, the taskforce has had a number of collaborative efforts with ISCB, including PLOS Topic Pages, an annual Wikipedia competition and events at ISCB conferences.

Despite the efforts of workforce members, the increasingly fast pace of the computational biology field means that many important Wikipedia articles are outdated or incomplete: more than 70% of relevant articles are marked as “start class” (developing but essentially incomplete) or lower. We firmly believe that improving relevant Wikipedia articles and therefore improving public access to information about our field is a professional responsibility for ISCB members.

ISCB Communities of Special Interest (COSIs) are self-organising communities of ISCB members focused on topics within computational biology. Connecting COSIs with relevant Wikipedia articles will: i) illuminate the current state of Wikipedia articles which COSI members will have a keen interest and specialised knowledge in; ii) provide a sense of ‘ownership’ of articles relevant to each COSI with COSI members particularly motivated to improve ‘their’ articles; iii) kickstart a wider push to improve coverage of computational biology on Wikipedia.

Project

We propose two major tasks for the hackathon.

• Our priority task is to conduct a review of the ~1,500 articles identified by the Computational Biology workforce, determining ISCB COSIs relevant to each article. This will allow a list of relevant articles for each COSI to be produced; each COSI can then focus on improving these articles using their specialist knowledge.
• A secondary task of the hackathon is to review the quality and relevance ratings of each article, based on Wikipedia’s content assessment guidelines. The last wide scale review of this type was conducted in 2011 and many articles have been modified without a corresponding change in their ratings.

Further ‘stretch goals’ of the hackathon may include identifying missing articles, and improvement of relevant articles tagged as requiring attention (currently around 40%)

We intend to spend some time discussing coordination with COSIs and planning follow-up events.

Registration/fees

The hackathon is open with no associated registration fee. The detailed zoom join-in link will be posted on this page, on ISCB Student Council Symposium 2021 and social media channels two days prior to the event. For any question please email the organisers at This email address is being protected from spambots. You need JavaScript enabled to view it..

Who can attend, required skills?

We invite all interested SCS attendees, student delegates of ISMB and student members of ISCB to attend.

Our priority task (1) will not require Wikipedia editing, so no previous editing background is required. Our secondary task (2) would benefit from familiarity with the Wikipedia content assessment guidelines but again will not require previous editing background.

Outcomes

We plan to generate a list of Wikipedia articles that can be distributed to each COSI, so that they can identify areas for improvement or missing articles. Depending on the progress on the secondary goal, we also plan to generate quantitative data on article quality by COSI, with a view to monitoring future improvements in quality.

We will publish an article reporting the outcomes of the hackathon in a science journal. The top contributors will be invited to co-author the paper with the organisers.

Prizes

Harvard Medical School Master of Biomedical Informatics (HMS-BI) Program and the ISCB Student Council have kindly sponsored five $100 prizes, which will be awarded based on a drawing to be held at the conclusion of the session.

To be eligible for the award, participants must attend the full hackathon session and demonstrate substantial high-quality contributions to the tasks.

Pre Reading

We suggest that attendees familiarise themselves with the list of ISCB COSIs (https://www.iscb.org/cms_addon/cosi_reporting_system/COSIs/). For the secondary task, familiarity with Wikipedia’s content assessment grades for article quality (https://en.wikipedia.org/wiki/Wikipedia:Content_assessment) and article importance (https://en.wikipedia.org/wiki/Wikipedia:Version_1.0_Editorial_Team/Release_Version_Criteria#WikiProject_priority_assessments) would be useful.

Technical support

Logistical support and Zoom meeting facilities will be provided by ISCB. Participants will be invited to a Slack channel for further discussion with each other and the organisers.

Organisers

• Alastair Kilpatrick, Bioinformatician at the Centre for Regenerative Medicine
• Farzana Rahman, Lecturer in Computer Science and Mathematics at City University of London
• Lonnie Welch, Stuckey Professor of Electrical Engineering and Computer Science at Ohio University

Sponsors

• Janssen Immunology

Janssen Immunology

www.janssen.com/immunology
At Janssen Immunology, we are relentlessly dissatisfied with the status quo, and are working to create a future where autoimmune diseases are a thing of the past. Our Immunology team is focused on redefining care by delivering transformational therapies and regimens to address unmet need in patients and restore balance in the immune system for those living with autoimmune disease. For more information or to learn about career opportunities, please visit https://www.janssen.com/immunology

Science Communication and Science Journalism

Tuesday, July 27 14:20 - 15:20 UTC
Organizers: Public Affairs & Policy Committee

Collaborative Tools for Protein Analysis Hackathon 2021

Introduction to Hackathon: Saturday, July 24, 10am-Noon UTC
Hackathon: 24-29 July 2021, Flexible Times
Final Project Presentations and Discussion: Thursday, July 29, 12:40 - 14:00 UTC
Organizers: Ravi Abrol, Philippe Youkharibache, Allissa Dillman, Jiyao Wang, Raul Cacha

There is no registration fee for the Hackathon@ISMB2021 beyond your normal ISMB/ECCB 2021 registration fees. You must be registered for ISMB/ECCB 2021 to participate in this hackathon.

Towards integrating protein sequence-structure-function analysis, visualization and open collaborative research

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

Preamble

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.

Potential Team Projects

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.

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

Registration and fees

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.

Who can participate and what skills are needed?

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.

Outcome

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.

Getting Started with iCn3D

1. PROGRAM:
   1. iCn3D publications: You can familiarize yourself with iCn3D through our recent publication and preprint.
   2. Try iCn3D now!
   3. iCn3D@GitHub
2. TUTORIALS and DOCUMENTATION
   1. iCn3D Tutorial Part 1 (the basics): Video, Slides
   2. iCn3D Tutorial Part 2 (molecular interactions, structural comparisons, etc): Video, Slides
   3. Full documentation (Help pages)

Technical and Project Support

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