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COSI Information

ISCB Communities of Special Interest (COSIs) are member communities of shared interest that have self-organized and have multiple activities or interactions throughout the year, rather than solely meeting during the ISMB conference in the COSI track. An important goal of any COSI is to foster a topically-focused collaborative community wherein scientists communicate with one another on research problems and/or opportunities in specific areas of computational biology. Such communication is often in the form of meetings, but can also be through other social media tools that allow for vibrant participation in a virtual environment. If you are interested in starting an ISCB COSI please review the COSI Guidelines and send your exploratory questions to Diane E. Kovats, ISCB Executive Director (dkovats@iscb.org

Communities of Special Interest (COSI) Groups


3D-SIG: Structural Bioinformatics and Computational Biophysics

3D-SIG focuses on structural bioinformatics and computational biophysics and has become the largest meeting in this growing field.

Leadership Structure
We added a proceedings chair for 3DSIG (Iris Antes).

Activities Over the Last Year
We set up a slack channel that currently has 172 members (compared to 123 last year).

Equity, Diversification, and Inclusion Efforts
The same as those of ISCB.

Web site: NA
Online Community group: Slack Channel

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Bio-Ontologies

Bio-Ontologies Special Interest Group (SIG) covers the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences.

Leadership Structure
Michel Dumontier is currently the COSI Committee Representative and the COSI track Chair. In 2020-2021, Michel Dumontier will remain the COSI Committee Representative and Núria Queralt Rosinach will replace Karin Verspoor as the alternate COSI Committee Representative. Robert Hoehndorf is currently the COSI Proceedings Liaison and alternate COSI Track Chair. In 2020-2021, Robert Hoehndorf will serve as the COSI Track Chair and alternate COSI Proceedings Liaison. Xiaolin Yang is currently the alternate COSI Proceedings Liaison and in 2020-2021 she will serve as the COSI Proceedings Liaison. Tiffany Callahan will serve as the alternate COSI Track Chair.

Activities Over the Last Year
Bio-Ontologies (#bioontologies; http://www.bio-ontologies.org.uk/) is an ISMB Community of Special Interest (COSI) that covers the latest and most innovative research in the application of ontologies and the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences.

Bio-Ontologies celebrated its 23rd year at ISMB 2020, held virtually on July 13-16, 2020. Bio-Ontologies provides a vibrant environment for reporting novel methods and sharing experiences on the construction and application of ontologies in health care and the life sciences. The COSI run track offers a constructive environment to nurture discussion of innovative and scientifically sound work that range from preliminary to completed, from both young and experienced investigators alike. Bio-Ontologies participants also benefit from a strongly interdisciplinary setting, where ISMB attendees intermingle with members from American Medical Informatics Association (AMIA), the W3C’s Healthcare and Life Sciences Community Group (HCLSCG), and the National COVID Cohort Collaborative (N3C) thereby increasing impact through new collaborations and broader dissemination.

Day 1 of the Bio-ontologies track included 2 keynotes: The first keynote was delivered by Dr. Michael Gruninger on “Bio-Ontologies Keynote: The crisis of content” where he shared his ideas for a novel approach for designing ontologies, which formalizes ontology semantics in order to guarantee shareability and reusability. In the second keynote, Dr. Karin Verspoor presented on “Bio-Ontologies Keynote: COVID-SEE: Enabling scientific evidence exploration through semantics in a time of crisis” where she discussed the development of COVID-SEE (Scientific Evidence Explorer), a novel NLP system designed to improving the processing and representation of COVID-19 related literature. Both talks drew sizable crowds and elicited lively discussions.

Bio-ontologies also featured many exciting talks on the application of ontologies and knowledge graphs in computational biology. The day featured 10 regular talks covering different uses of ontologies for COVID-19 (i.e. development of new ontologies, methods for modeling quantitative traits, and collection and analysis of animal hosts and diagnosis), FAIR (i.e. ensuring reproducible data analysis and metadata standards for sharing knowledge graph embeddings), text mining (i.e. ontology-based information extraction and fact-tracking), data analysis (ontology-wide association studies to enrich traditional GWAS analyses), knowledge representation (for human pluripotent stem cell lines, and for physician suicide claims as nanopublications), and the development of biomedical knowledge graph construction software.

Day 2 (half day) of the Bio-ontologies track featured 5 talks primarily focused on the development of novel ontology-based tools designed to detect Gene Ontology misannotations, improve the ontology development process, model biological phenomena, and enrich models of human disease. The session closed with a call to participate in the 2021 proceedings and in further development of the COSI’s planned activities.

This year’s talks had a clear new trend topic: “COVID-19/infectious diseases” due to the challenge posed by the COVID-19 pandemic, which is consistent with the massive amount of research effort the scientific community is devoting to meet this urgent societal need and highlights the importance of ontologies in biomedical research. The kind of papers presented covered a wide range of biomedical areas, from clinical to omics, and applications, from NLP to FAIR enabler. Best talk was awarded to Runar Reve for his work on Applying GWAS on UK Biobank by using enhanced phenotype information based on Ontology-Wide Association Study and best poster was awarded to Toshiyuki T. Yokoyama and Simon Heumos for their work on Semantic Variation Graphs: Ontologies for Pangenome Graphs.

The COSI sessions also had social media impact on Twitter (activity under #BioOnt2020 tag) and on Slack (11 new members registered on the bio-ontologies workspace).

Equity, Diversification, and Inclusion Efforts
- Gender representation: COSI track succeeded in obtaining good gender balance (47.1% Female, 52.9% Male);
- World research representation: The majority of Bio-Ontology COSI researchers were from North America (47.1%), followed by Europe (23.5%), Asia (11.8%), the Middle East (11.8%), and Oceania (5.9%);

Web site: http://www.bio-ontologies.org.uk/
Online Community group: http://www.bio-ontologies.org.uk/

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BIOINFO-CORE

Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas. We share knowledge, practices, business tips and analytic trends.

Leadership Structure
The Organizing Committee continues to include Brent Richter, Madelaine Gogol, Alastair Kerr, Hemant Kelkar, and Alberto Riva, Daniel Stekhoven, and Rodrigo Ortega Polo.

Brent Richter - Mass General Brigham, United States - <brichter@partners.org>
Madelaine Gogol - Stowers Institute, United States - <mcm@stowers.org>
Alastair Kerr - CRUK-MI, University of Manchester, United Kingdom - <alastair.rw.kerr@gmail.com>
Alberto Riva - University of Florida, United States - <ariva@ufl.edu>
Rodrigo Polo - Lethbridge Research and Development Centre of Agriculture and Agri-Food Canada - <rodrigo.ortegapolo@canada.ca>
Daniel Stekhoven - Swiss Institute of Bioinformatics - <stekhoven@nexus.ethz.ch>

Activities Over the Last Year
The BIOINFO-CORE COSI held a virtual session exploring both present and perennial topics, including spatial transcriptomics, single cell analysis, bioinformatic capacity building, and mentoring and management of bioinformatics cores. In small breakout groups, participants were able to meet colleagues from diverse cores, functions and backgrounds and discuss these topics in greater depth. The discussions were presented to the room and we look forward to our upcoming café connect zoom meetup for further sharing and brainstorming. Please see our wiki for more details, slides and notes. (http://bioinfo-core.org/).

Our speakers in the session at ISMB 2020 were:

BioNet Alberta: A network based approach to Bioinformatic capacity building in Alberta. Eric Merzetti, University of Lethbridge, Canada.
Mentoring and Managing Staff in Bioinformatics Cores. Krishna Karuturi, The Jackson Laboratory, United States
Chickens in Space: our experiences with spatial transcriptomics on the 10x Visium and slide-seq platforms. Madelaine Gogol, Stowers Institute, United States.
Multi-sample, multi-condition analysis in scRNAseq data sets. Simone Marini, University of Florida, United States.

Equity, Diversification, and Inclusion Efforts
BIOINFO-CORE recognizes the ISCB code of conduct which enshrines the values for equity, diversity and inclusion.

Web site: http://www.bioinfo-core.org/

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BioVis: Biological Data Visualizations

Data visualization cuts across all areas of computational biology. On the one hand, sophisticated data visualization techniques are required to allow the biologist to explore their large/complex datasets and gain insight from them. On the other hand, this approach can lower the black-box nature of complex (bioinformatics) algorithms. The goal of BioVis is to bring together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging bioinformatics and biology researchers in state-of-the-art visualization research, as well as visualization researchers in problems in biological data visualization.

Leadership Structure
BioVis 2020 General Chairs

Cagatay Turkay, University of Warwick, UK
Michel Westenberg, Eindhoven University of Technology, Netherlands

Steering Committee

Kay Nieselt, University of Tuebingen, Germany (Chair)
Jan Aerts, Hasselt University, Belgium
Liz Marai, University of Illinois at Chicago, USA
Jim Procter, University of Dundee, United Kingdom
Marc Streit, Johannes Kepler University Linz, Austria

Activities Over the Last Year
Number of invited keynotes: 2
Number of abstract talks: 24
Number of abstract submissions: 14
Number of proceedings talks: 2
Number of posters: 17
Sponsorship obtained: None

Highlights of the scientific/enabling themes from the meeting (i.e., the half page article for the Society pages, newsletter, and annual report):
The 10th edition of BioVis (http://biovis.net/2020/program_ismb/) attracted over 380 unique viewer participants and there were 335 registrants showing interest in BioVis. Along this year’s theme of "Integrating visualization and machine learning and explainable AI for biological analysis", we had two great keynotes by Hendrik Stobelt (IBM Research & MIT) and Marinka Zitnik (Harvard Medical School). We started with Hendrik’s talk on the importance of visualization for human-AI collaboration where he presented projects from the IBM Explainability Team. In the afternoon, Marinka gave an inspiring and very popular talk on Machine Learning for Drug Repurposing and presented an impressive range of projects that sparked several questions and a lively discussion. There were over 150 live participants during Marinka’s talk.

The program featured a further 2 full papers presenting innovation in visualisation, 14 abstract talks and 17 poster presentations concerning the latest developments in visual analysis systems that tackle biological data, from phylogenetic trees to SNP data. The award for the best poster went to Kari Lavikka and colleagues for their work titled “Grammar-Based Interactive Genome Visualization”. The “interactive” sessions following the talks were very popular and several participants carried out their discussions in the Zoom calls in-between the sessions. The social channel was particularly busy after Marinka’s talk.


Plans for ISMB 2021
- Number of days needed: 1
- Possible sponsorship: We plan to raise $3K-$10K.
- Program highlights if known: not yet finalized, we plan to have a thematic focus either on scRNA data visualisation or on the topic of BioVis meets Medicine.

Other activities:

The group also carries out the annual BioVis Challenges Workshop at the IEEE VIS conference -- the premier visualisation conference. The goal of the Biological Data Visualization Challenges Workshop (BioVis Challenges Workshop) is to educate, inspire, and engage visualization researchers in current problems in biological data visualization. The fourth iteration of the workshop has been held on October 26th 2020 at VIS as a virtual event (http://biovis.net/2020/program_ieee/). The workshop followed the challenges format where the day started with expert talks and continued with challenge entry talks.

Equity, Diversification, and Inclusion Efforts
BioVis strives to achieve equity and diversity both in its management and operational structures. We actively recruit junior members of the community to organisational roles and offer more senior roles as they gain experience. We aim to achieve a gender balance in the curation of the organising committees and also in curating the programme where we have control. In curating the invited talk programme, for instance, we aim for a gender balance as is evidenced from the keynote selections in the past five years where we always had a male and a female invited keynote speaker.

Web site: http://biovis.net/
Online Community group: https://groups.google.com/a/iscb.org/g/biovis.cosi

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BOSC: Bioinformatics Open Source Conference

Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics and open science. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, reproducible results and software; and ways to grow open source communities while promoting diversity within them. BOSC is run by the Open Bioinformatics Foundation (OBF).

Leadership Structure
The Open Bioinformatics Foundation (OBF), which is the parent organization of BOSC, is led by an elected Board that currently includes 8 members (https://www.open-bio.org/board/).
There were several changes to OBF leadership in December 2019 (see https://www.open-bio.org/2020/01/14/obf-board-elections-december-2019/):
- Hilmar Lapp: stepped down after 8 years as President of the Board; elected to At-Large seat.
- Peter Cock: elected as President of the Board.
- Heather Wiencko: elected as Treasurer, replacing previous Treasurer Peter Cock.

BOSC (https://www.open-bio.org/events/bosc/) continues to be chaired by Nomi Harris. For 2021, the co-chair is Karsten Hokamp. The rest of the organizing committee, including some new and some returning members, can be found at https://www.open-bio.org/events/bosc-2021/

Activities Over the Last Year
Accomplishments of the OBF over the past year include:
- Clarified the process of becoming an OBF Affiliated Project (https://github.com/OBF/obf-docs/blob/master/Affiliated-Project-Policy.md)
- Participated in Google Summer of Code 2020 (https://summerofcode.withgoogle.com/archive/2020/organizations/4595548239167488/. 8 students worked on open source bioinformatics-related projects, with 18 mentors and four organisation admins managing the program and work. (https://www.open-bio.org/2020/11/04/google-summer-of-code-2020-wrap-up/)
- Travel Fellowships:
-- In December 2019, Malvika Sharan took over as OBF Travel Fellowship chair, replacing previous chair Farah Khan (https://www.open-bio.org/2019/12/21/travel-fellowship-december-2019/)
-- Expanded the Travel Fellowship program (now renamed the OBF Event Fellowships) to cover costs associated with participating in online events such as virtual conference fees, headsets, high speed internet, etc. (https://www.open-bio.org/event-awards/)
-- Revised the Event Fellowship application calendar; applications are now reviewed twice a year (April and October).
-- In the past year, 7 people were awarded funds to attend in-person or virtual events. 2 applicants received funding in the December 2019 round, 4 in the April 2020 round (https://www.open-bio.org/2020/05/08/obf-travel-fellow-2020-1/), and 1 in the October 2020 round.
- Developed an OBF-wide Code of Conduct that apply to in-person and virtual events organised and led by OBF, and can be adopted by member projects if they choose. The proposed Code of Conduct is still open for community comments at https://github.com/OBF/obf-docs/pull/78

BOSC accomplishments over the past year include:
- Development of a comprehensive document covering the BOSC abstract review process: https://github.com/OBF/bosc_materials/blob/master/BOSC_review_process.md
- BOSC 2020: Most years, BOSC has been part of ISMB, but in 2018, and again in 2020, BOSC partnered with the Galaxy Community Conference (GCC). This year (in July 2020), the BOSC + GCC conference was called the Bioinformatics Community Conference (BCC2020, bcc2020.github.io). More than 800 people from 61 countries registered for at least part of the online meeting, which was held mostly in the Remo.co video-conferencing platform. Keynote speakers were Abigail Cabunoc Mayes, Lincoln Stein, and Prashanth Suravajhala. The BOSC 2020 schedule can be found at https://www.open-bio.org/events/bosc/schedule/. A report about BOSC 2020 can be found on F1000: https://f1000research.com/articles/9-1160

Equity, Diversification, and Inclusion Efforts
- The OBF continually strives for greater inclusion both within OBF-sponsored events and across the broader open bioinformatics community. Our Event Fellowship program is specifically aimed at improving diversity at bioscience related events by supporting people from groups that are traditionally underrepresented in bioinformatics. One of the revisions we made to the Event Fellowship assessment process to improve equity is that applications are now reviewed with a standard rubric and without the applicants’ names, to reduce the chance of unintentional reviewer bias. Another recent effort aimed at promoting diversity, inclusion and equity has been the development of a community-approved Code of Conduct described above.
- Efforts to make BOSC 2020 accessible and inclusive included very low registration fees (which were set even lower for participants from lower-income countries), talks presented twice a day so that people from around the globe could participate, and closed captioning for all videos. These efforts are at least partly to thank for the greatly increased number of participants from around the world, including many from outside of Europe & North America. For more details, please see https://f1000research.com/articles/9-1160
- The revised BOSC review process aims to support equity by ensuring fair, consistent, and constructive abstract reviews, regardless of the identity of the submitting authors and reviewers. As part of the process, all reviewers are required to read and agree to the conference’s Code of Conduct.

Web site: https://www.open-bio.org/events/bosc/
Online Community group: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew

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CAMDA: Critical Assessment of Massive Data Analysis

CAMDA presents a crowd sourcing and open-ended data analysis challenge format which focuses on big heterogeneous data sets that are increasingly produced in several fields of the life sciences.

Leadership Structure
CAMDA is co-chaired by Wenzhong Xiao (Harvard/Stanford), Joaquin Dopazo (Spanish Health Ministry), David Kreil (Vienna). In recent years, Pawel Labaj, a young group leader at a top university in Poland joined the board as co-chair.
The chairs are supported by a Scientific Committee which features a good mix of senior established researchers like Wolfgang Huber and young talend in the field. We are actively working to invite additional young promising members. This year the Scientific Committe was joined by Maria Pena Chilet. She is a highly cited young researchers in Andalusia.

Activities Over the Last Year
The challenges for CAMDA 2020 were advertised early in the year and included:
The Hi-Res Cancer Data Integration Challenge presents clinical and matched molecular profiles, with read level data for individual genomes. Explore non-standard genomes and splicing events for better prognosis. Where download is not feasible, data can be made available on hard-disk by courier.
The CMap Drug Safety Challenge presents clinical toxicity results, cellular and molecular responses to hundreds of drugs. Compare and integrate a range of cell line assays to predict the severity of the drug induced liver injury in humans.
The Metagenomic Geolocation Challenge presents thousands of city microbiome profiles in context of climate data. Construct multi-source microbiome fingerprints and predict the ecological niche or exact geographical origin of mystery samples.
This year, CAMDA with ISMB for the first time ran as a virtual conference due to the recend pandemic. Virtual CAMDA 2020 took off to a full house, with the almost 200 delegates likely grateful that they didn't have to cram into a real room, while reducing their carbon footprint by 100 tons of carbon dioxide. Opening the session, former NSF director Prof. Rita Colwell show-cased in her keynote on cholera the power of multi-level analyses ranging from microbial meta-genomics via public health to climate-scale effects, which was followed by a variety of contributions by CAMDA delegates dissecting the interactions of urban microbial meta-genomics and ecological climate niches. Daena Farber's Aedin Culhane started the second day of CAMDA with a much-anticipated keynote on cancer single-cell -omics data-integration and factor analyses, giving a practical tour de force of current algorithmic alternatives, which was followed by contributions of CAMDA delegates on challenging cancer data sets and drug safety predictions. While the traditional real-world CAMDA dinner was sorely missed this time, as every year, the last session closed with a ceremony where promising young scientists accepted the treasured CAMDA Awards, which was nicely put into context by Joaquin Dopazo marking the CAMDA 2000-2020 anniversary with a perspective of how the 'Critical Assessment of Massive Data Analysis' pioneered the crowd-sourcing of science, showing the way with open ended questions in scientific data analysis competitions, which naturally segued into Wenzhong Xiao leading a discussion of current challenges in Big Data analyses for CAMDA 2021 and beyond.

Equity, Diversification, and Inclusion Efforts
Both keynotes at CAMDA 2020 were female: Rita Colwell, Distinguished University Professor and former Director of the US National Science Foundation. Aedin Culhane is a rising group leader at Daena Farber Cancer Institute and the Dept of Biostatistics in Harvard.
CAMDA featured speakers from: Australia, Bulgaria, Canada, Poland, South Korea, Spain, and U.S.A.

Web site: www.camda.info
Online Community group: https://groups.google.com/a/iscb.org/g/camda.cosi

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CompMS: Computational Mass Spectrometry

The CompMS COSI promotes the efficient, high quality analysis of mass spectrometry data through dissemination and training in existing approaches and coordination of new, innovative approaches. The CompMS initiative aims to exploit synergies between different mass spectrometry-based application domains, in particular proteomics and metabolomics.

Leadership Structure
The CompMS leadership consists of Wout Bittremieux (University of California San Diego), Timo Sachsenberg (University of Tübingen), Isabell Bludau (Max Planck Institute of Biochemistry), and Lindsay Pino (University of Pennsylvania).

Activities Over the Last Year
At ISMB 2020 the CompMS COSI received 49 abstract submissions, up from 10 and 21 abstract submissions in 2018 and 2019, respectively. This prompted us to expand the CompMS program at ISMB to two days for the first time. The first day was focused on proteomics applications and included a mix of eight short (10 minutes) and nine long (20 minutes) presentations on various topics, including public data repositories, mass spectrometry imaging, spectral clustering, and spectrum identification and quantification. A very timely keynote was delivered by Dr. Anne-Claude Gingras on the SARS-CoV-2 virus-host interactome.
The second day was focused on metabolomics applications and was guest hosted by Dr. Shuzhao Li and Dr. Jeff Xia. It included five short talks and four long talks. Keynote presentations were delivered by Dr. David Wishart on computational tools to identify the dark metabolome and by Dr. Gary Siudzak on repository-scale metabolomics analysis. Getting more engagement from the metabolomics community has been a goal for the CompMS COSI, and we are delighted that we were able to devote an additional day to metabolomics topics for the first time.
Besides the oral representations, 27 abstracts were selected as poster presentations. Two of the poster presentations were awarded a best poster prize and two oral presentations were awarded a best presentation prize (one proteomics and one metabolomics poster/oral presentation each).
The CompMS session was well attended, with the number of participants on each of the two days hovering around 60 people. Break-out sessions in addition to the officially scheduled presentations were only sparsely attended, although some interesting discussions took place. Given the unprecedented number of abstract submissions, session attendees, and the expansion of the CompMS program from one to two days, despite the challenges posed by the SARS-CoV-2 pandemic, the CompMS COSI at ISMB 2020 was very successful.

Besides the CompMS COSI session at ISMB 2020, the May Institute on Computation and Statistics for Mass Spectrometry and Proteomics was sponsored by CompMS and attracted over 100 participants.

Equity, Diversification, and Inclusion Efforts
To promote diversity we have surveyed the computational mass spectrometry community via Twitter to provide recommendations for our keynote speaker from female, minority, or other under-represented groups. After recent changes, leadership for the CompMS COSI is gender-balanced. Additionally, all four current members of the CompMS COSI leadership are early-career researchers and we strongly commit to promoting the work of early-career researchers.

Web site: http://compms.org/

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Education: Computational Biology and Bioinformatics Education and Training

The ISCB EDUCATION COSI focuses on bioinformatics and computational biology education and training across the life sciences. A major goal of this COSI is to foster a mutually supportive, collaborative community in which bioscientists can share bioinformatics education and training resources and experiences, and facilitate the development of education programs, courses, curricula, etc., and teaching tools and methods.

Leadership Structure
Education COSI Chairs: Russell Schwartz (Chair, Carnegie Mellon University, USA), Patricia Palagi (SIB Swiss Institute of Bioinformatics, Switzerland), Annette McGrath (CSIRO, Australia).

Activities Over the Last Year
The COSI works to bring bioinformatics education to the agenda of the ISCB community and to export it to education efforts in computational biology and life sciences internationally. It started with an agenda of specifically bringing together the ISCB Education community with the Global Organisation for Bioinformatics Learning, Education & Training (GOBLET), although it has since broadened its mission to be an interface between the ISCB education community and the international bioinformatics education community broadly defined..

The largest single effort of the COSI each year is the ISCB educational program and associated activities, where the COSI seeks to create a community discussion on education within ISMB, bring in voices from outside ISCB to work with us, and highlight some of the most exciting work in the field each year. The COSI also works with the Workshop on Education in Bioinformatics (WEB) to offer an integrated ISMB program in recent year. As in previous years, this combined COSI program led to a vibrant program 1.5-day program of invited and submitted talks, posters, and workshop sessions. COSI members also contributed to organizing the tutorial program at ISMB.

The COSI also works to bring education topics to other meetings of the community. While 2020 has been a bad year for meetings and opportunities and our opportunities have been fewer, we have remained active in encouraging members to bring education topics to other meetings they attend. Examples include Schwartz ensuring that education would be covered as part of a panel discussion on the Future of Algorithms in Biology at RECOMB when he served as RECOMB PC Chair this year.

The COSI has also been very active in a series of collaborative education initiatives organized around what has become an annual Bioinformatics Education Summit, held virtually this year. The summit, led by Nicky Mulder, has been organizing several prominent efforts in bioinformatics education now to define and improve standards for bioinformatics education, to produce papers and other resources and training materials for the community, and to work with the ISCB on initiatives such as the short course affiliation and degree program endorsement processes now being put in place. The COSI is one of several sponsoring groups of this summit and active in its organization and planning and running sessions, developing the materials it has produced, and working offline on continuing to refine that work and prepare it for dissemination.

The COSI leadership is also represented on leadership meetings of the ISCB's education community and remains active in ongoing ISCB education initiatives. Schwartz participates in monthly leadership meetings with other ISCB education community members on this work.

Equity, Diversification, and Inclusion Efforts
We have sought to promote Equity, Diversity, and Inclusion through consideration for a diverse and inclusive selection of speakers for the education COSI program at ISMB each year. For example, the program's 12 speakers this year featured 7 women (1 of 2 keynotes and 6 of 10 submitted talks) and 3 presenters from low-income countries. Membership in the COSI is open to anyone interested in the topic and so we do not specifically select for diversity, but strive to be welcoming to all.

Web site: https://groups.google.com/a/iscb.org/forum/#!forum/education.cosi
Online Community group: https://groups.google.com/a/iscb.org/forum/#!forum/education.cosi

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EvolCompGen: Evolution & Comparative Genomics

Evolution and comparative genomics are deeply intertwined with computational biology. Computational evolutionary methods, such as phylogenetic inference methods or multiple sequence alignment are widely used, yet remain far from “solved” and are indeed intense areas of research. At the same time, evolutionary and comparative genomics are inherently “transversal” disciplines in that work in many other biological areas of research have some evolutionary component (e.g. cancer genomics, epidemiology, toxicology, population genetics, functional genomics, structural biology just to name a few). The scope of this COSI is intentionally kept broad. The track will feature a mix of proceedings, highlight, and invited talks. Priority will be given to contributions which are relevant to more than a single area of application, or to contributions which are not covered by more specialised COSIs.

Leadership Structure
COSI chair: Nadia El Mabrouk (substitute: Christophe Dessimoz)
Nominated as Proceedings Area Chairs: Dannie Durand and Wataru Iwasaki
Abstract chairs: Giltae Song, Janani Ravi, Edward Braun
Award chair: Louxin Zhang and Celine Scornavacca
Communication/website: Lars Arvestad
Webinar: Bart Cuypers and Aida Ouangraoua

Activities Over the Last Year
The Evolution and Comparative Genomics (EvolCompGen) COSI hosted a one day-session at ISMB 2020. The session featured a stimulating mix of proceedings and contributed talks on a wide variety of topics, befitting the central role of evolution in the biological sciences. The talks touched on timescales as short as those for viral epidemics and the progression of cancer to those as long as the complete history of life on Earth Computational topics included species tree estimation, phylogenetic tree comparison, modeling protein sequence evolution, and reconstructing genome rearrangements.
The COSI (and in particular Aida Ouangraoua) was instrumental in helping ISCB to set up its webinar series on evolution and comparative genomics topics in collaboration with the Society of Molecular Biology and Evoluion (SMBE). In the past year, our COSI hosted four talks. Importantly, the participation is free for any members of ISCB and SMBE.

Many members of our COSI are also in leadership roles at RECOMB-CG.

Equity, Diversification, and Inclusion Efforts
Our COSI is open to all interested members of the research community. In our leadership, we have good gender, ethnic, geographic. Our committee includes two early career researchers (Janani Ravi and Bart Cuypers).

Web site: https://evolcompgen.org
Online Community group: https://ismb-evolcompgen.slack.com/

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Function: Gene and Protein Function Annotation

The accurate annotation of protein function is key to understanding life at the molecular level. The Function SIG COSI brings together computational biologists, experimental biologists and biocurators who are dealing with gene and gene product function prediction, to share ideas and create collaborations. The Function-SIG holds annual meetings and conducts the multi-year Critical Assessment of protein Function Annotation, or CAFA, experiment.

Leadership Structure
Track Chairs: Iddo Freidbery, Kimberley Reynolds, Mark Wass
The Critical Assessment of Functional Annotation (CAFA) is closely associated with Function COSI. The CAFA organisers are: Iddo Friedberg, Predrag Radivojac, Casey Green, Sean Mooney

Activities Over the Last Year
The Function Community of Special Interest (COSI, http://www.biofunctionprediction.org) covers the lastest developments in the computational biology applications to functional annotation of proteins and understanding protein function.

At ISMB2020 the Function COSI held its 14th meeting, and first virtual meeting. The meeting started with a keynote from Nobel laureate, Dr Richard Robert who spoke about "DNA methylases – computation, experiments and new biology". The second keynote presentation was given by Carolyn Lawrence-Dill and focussed on "Saving Time at the Bench and in the Field: Predicting Gene Function and Phenotype in Crops". Gary Bader spoke about "Gene function prediction using unsupervised biological network integration" in the third keynote.

The two day Function track also saw the presentation of three proceedings paper ranging in topic from negative examples for training protein function prediction methods to investigating the orthologue conjecture. There were also 15 talks selected from submitted abstracts, which again covered diverse topics within Function including the identification of moonlighting proteins and updates on functional annotation within UniProt.

The Critical Assessment of Functional Annotation (CAFA) is a central element of the Function COSI. The fourth round of the assessment (CAFA4) launched in September 2019 with participants submitting predictions in February 2020. We were impressed by the growing level of interest in the CAFA challenge and the Function COSI. The initial results from CAFA4 were presented at the meeting along with talks from some of the top performing groups. Additionally, the results from CAFA3 were published in Genome Biology, with 167 co-authors, most of which are COSI members.

We have recently applied for continuing NSF funding based on the community growth, with 72 letters of support we solicited from the labs participating in the CAFA challenge and the Function COSI. We have held one Zoom call with some 30 members of the community and are collaborating on a manuscript on refining the assessment procedure in the CAFA competition.

Equity, Diversification, and Inclusion Efforts
The organising committee makes an effort to identify a diverse range of Keynote speakers and also for the selection of oral presentations from selected abstracts.

Web site: https://www.biofunctionprediction.org/

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HiTSeq: High Throughput Sequencing Algorithms & Applications

HiTSeq is devoted to the latest advances in computational techniques for the analysis of high-throughput sequencing data including novel algorithms, analysis methods and applications in biology where high-throughput sequencing data has been transformative. It provides a forum for in depth presentations of novel algorithms, analysis methods, and applications in multiple areas of biology that HTS is transforming.

Leadership Structure
This year we added to new co-chairs to the organization structure: Layla Oesper and Gang Fang.

Activities Over the Last Year
Mostly focused on organizing the ISMB session of HiTSeq. We explored the idea of having affiliated local meetings, but with COVID we have not been able to explore this much. Nevertheless, HiTSeq held an online regional meting in the Bay Area in conjunction with the Bay Area Bioinformatics Forum group, and Stanford University, on COVID Bioinformatics. (https://www.meetup.com/BayBIFX/events/270179841/). This is adoption that we want to explore further.

Equity, Diversification, and Inclusion Efforts
We strive to add additional co-chairs from all backgrounds and regions and ensure female co-chairs are recruited. We also strive to balance the keynote invitations that have equal numbers of female and male speakers. Final keynote speakers depende on acceptance to our invitations. Abstracts for talk are selected purely on a score basis, and authors decide who presents at the conference.

Web site: http://hitseq.org
Online Community group: N/A

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IRNA: Integrative RNA Biology

The iRNA COSI aims to bring together experts in computational and experimental aspects of research in RNA Biology to cover new developments across this broad field of research. The iRNA meeting at ISMB focuses on two major areas: (1) the development of computational and high-throughput experimental methods, and (2) the application of such methods to break new grounds in the study of RNA biology and disease. Through the meetings and various online activities we aim to educate and inspire researchers in the field, novice and seasoned alike, by meshing together different aspects of Computational RNA Biology, and promoting cross-disciplinary collaborative research.

Leadership Structure
2020 Organizing Committee
Yoseph Barash, University of Pennsylvania, USA
Klemens Hertel, University of California Irvine, USA
Michelle Scott, Université de Sherbrooke, Canada

2020 Abstract Committee
Klemens Hertel, University of California Irvine, USA
Yoseph Barash, University of Pennsylvania, USA
Michelle Scott, Université de Sherbrooke, Canada

2020 Proceedings Chair
Jérôme Waldispühl, McGill University, Canada

Activities Over the Last Year
Scientific highlights of the RNA COSI at ISMB 2020
The 2020 iRNA COSI track brought together world experts in diverse aspects of computational RNA biology from RNA structure, RNA-seq, RNA splicing and RNA processing to non-coding RNAs and RNA networks. The iRNA COSI aims also to promote interactions between computational and experimental RNA biologists and encourages participation from groups that are more experimental in nature. The 2020 RNA COSI track featured 18 talks (including 3 keynotes) highly computational in nature and 9 talks (including 1 keynote) with stronger experimental input.

This year we had an exciting line-up of 4 keynotes that covered transcriptomics (including a keynote presentation by Ana Conesa from the University of Florida), noncoding RNA biology, RNA metabolism (with a keynote from Athma Pai from the University of Massachusetts Medical School), RNA alignments and structure prediction (with a keynote presentation from Jérôme Waldispühl from McGill University) and RNA subcellular localization (with a keynote from Éric Lécuyer from the Montreal Clinical Research Institute). These keynotes invigorated very exciting sessions with talks from selected abstracts and proceedings in these and other topics, including tools and analyses of alternative splicing, RNA editing, RNA family classification, RNA-protein interactions, single cell and long-read sequencing analyses and methods for RNA secondary structure prediction.

Despite the difficulty in organizing such an event virtually, the iRNA COSI carried out a successful interactive poster session with presenters in breakout rooms and participants visiting rooms, leading to stimulating discussions with up to 6-7 people. In addition, while no in person conference dinner took place, we had a fun cocktail session at the end of our first day, complete with our traditional quiz, which participants enjoyed. Finally, a highlight of this year’s iRNA COSI was definitely our live and animated panel discussion on long read RNA-seq, which was well attended and led to very insightful exchanges on a subject of wide current interest.

Year-round activities
-Upgrade and management of the iRNA COSI website to inform and mobilize the community: https://irbgroup.org/
-Strong participation in the ISCB Academy, with 6 seminars hosted by the iRNA COSI. This initiative is driven by several PhD/postdoc members, but in particular Mathieu Quesnel-Vallière. We also recruited the RNApuzzles group who will start organizing seminars within the iRNA COSI through the ISCB academy in the next few months.

Equity, Diversification, and Inclusion Efforts
When choosing our COSI keynote speakers, we spend time searching for members of our community who conduct excellent research but might not be sought after speakers (yet), a good proportion of which are members of minorities. When selecting abstracts for our talks, we always consider simultaneously EDI and scientific excellence. Including all researchers that see themselves as computational RNA scientists regardless of their origin is a fundamental principal of our COSI and we are completely convinced that increasing diversity in members increases diversity in ideas, enriching our community.

Web site: https://irnacosi.org/

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JPI: Junior Principal Investigators

Transitioning from a post-doc to a junior PI can be a challenging process requiring careful planning. Once running a group, junior PIs are faced with many new tasks, some of which are learnt on the job. The Junior Principal Investigators group (JPI) aims to provide support during this process via a community of peers.

Leadership Structure
Shaun Mahony and Anthony Gitter are currently leading JPI, while Lucia Peixoto recently rotated out of the leadership.

Activities Over the Last Year
JPI's activities focus on peer mentoring and resource sharing for junior faculty in computational biology. We primarily carry out these activities on dedicated channels in the New PI Slack group. For example, we have 34 ISCB members in the New PI Slack #iscb_jpi channel. This year, we had additionally planned a "Birds-of-a-Feather" session at ISMB, which was to be focused on funding opportunities for junior faculty. Unfortunately, most of our speakers (program officers at various funding agencies) cancelled due to COVID-related disruptions. Instead, we ran several Zoom-based social activities at ISMB 2020. We hope to resume informational sessions at ISMB 2021.

Equity, Diversification, and Inclusion Efforts

Web site: http://cosi.iscb.org/wiki/JPI:Home
Online Community group: https://newpislack.wordpress.com

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Microbiome

The MICROBIOME Community of Special Interest aims at the advancement and evaluation of computational methods in microbiome research, especially metaomic approaches. Based on the Critical Assessment of Metagenome Interpretation (CAMI), the COSI supplies users and developers with exhaustive quantitative data about the performance of methods in relevant scenarios. It therefore guides users in the selection and application of methods and in their proper interpretation. Furthermore, the COSI provides a platform for exchange and networking between method developers, and provides valuable information allowing them to identify promising directions for their future work.

Leadership Structure
Alice McHardy; Helmholtz Centre for Infection Research; alice.mchardy@helmholtz-hzi.de
Alexander Sczyrba; University of Bielefeld; asczyrba@cebitec.uni-bielefeld.de
No changes to structure

Activities Over the Last Year
We organized and continue to organize the second round of CAMI benchmarking challenges, as well as organized a CAMI challenge evaluation workshop in Brunswick in March 2020.

Equity, Diversification, and Inclusion Efforts
The COSI invited an equal number of male and female speakers. As COSI proceedings and keynote speaker, we invited an excellent scientist from Asia to increase geographic diversity.

Web site: https://www.microbiome-cosi.org/
Online Community group: https://groups.google.com/g/microbiome-cosi

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MLCSB: Machine Learning in Computational and Systems Biology

MLCSB is a community for researchers interested in the interface of data sciences and life sciences, in particular the method development and application challenges that arise for Machine Learning in Computational and Systems Biology.

Leadership Structure
Magnus Rattray and Chloe-Agathe Azencott are MLCSB co-presidents and are supported by the MLCSB board

Activities Over the Last Year
We have hosted two ICSB webinars: April 22, 2020 - DNCON2: improved protein contact prediction using two-level deep convolutional neural networks by Jianlin Chen, University of Missouri; August 11, 2020 - Protein Function Prediction using Graph Convolutional Networks with Language Model Features by Vladimir Gligorijevic, Flatiron Institute. As well as running the MLCSB COSI, we also support the MLCB meeting which is now a standalone meeting, typically US-based.

Equity, Diversification, and Inclusion Efforts
MLCSB encourages diversity and representation within its leadership. The MLCSB meeting has had male and female co-chairs in 2019, 2020 and 2021 and has female and male co-presidents.

Web site: http://cosi.iscb.org/wiki/MLCSB:Home
Online Community group: https://groups.google.com/a/iscb.org/g/mlcsb.cosi

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NetBio: Network Biology

As more research fields turn to network visualization and analysis for perspective, our Network Biology Community serves to introduce novel methods and tools, identify best practices and highlight the latest research in the growing and interconnected field of network biology.

Leadership Structure
Natasa Przulj
ICREA Research Professor at Barcelona Supercomputing Center
Professor, Computer Science, University College London
Member of the Academia Europaea
Member of the Serbian Royal Academy
Fellow of the British Computer Society Academy of Computing
https://life.bsc.es/iconbi/
NetBio COSI Chair

COSI Committee

Tijana Milenkovic
Frank M. Freimann Collegiate Associate Professor of Engineering
University of Notre Dame
Board of Directors, International Society for Computational Biology
https://nd.edu/~tmilenko/
NetBio COSI Track Chair
NetBio COSI Proceedings Liaison

Marinka Zitnik
Assistant Professor
Harvard University
https://zitniklab.hms.harvard.edu/
NetBio COSI Track Chair
NetBio COSI Committee Representative

Martina Summer Kutmon
Assistant Professor
Maastricht University
https://www.maastrichtuniversity.nl/martina.kutmon
NetBio COSI Abstract Selection Chair

Anaïs Baudot
Principal Investigator
CNRS Researcher
Aix Marseille University
https://www.marseille medical genetics.org/a baudot/
NetBio COSI Committee Representative

Scooter Morris
Executive Director, Resource on Biocomputing, Visualization, and Informatics
Adjunct Assistant Professor
University of California, San Francisco
https://www.cgl.ucsf.edu/home/scooter/
NetBio COSI Finances
NetBio COSI Abstract Selection Committee

Frank Kramer
Professor
University of Augsburg
https://informatik.uni augsburg.de/
NetBio COSI Abstract Selection Committee

Noel Malod Dognin
Established Researcher
Barcelona Supercomputing Center
Honorary Senior Research Associate
University College London
http://www.black wind.com/
NetBio COSI Website and Calendar Manager

Zainab Al Taie
PhD Student
University of Missouri Columbia
https://www.linkedin.com/in/zainab altaie/
NetBio COSI Communication, Publicity and Outreach

Activities Over the Last Year
The key activity in 2020 was the organization of the NetBio COSI at ISMB 2020. We had a large number of quality submissions, much larger than usual. Hence, we held the NetBio COSI at ISMB 2020 for a day and a half for the first time, while previously it was one day only. We are very happy about the expansion of the community, which is why we have requested and got approved a 2-day slot for the NetBio COSI at ISMB/ECCB 2021.

Equity, Diversification, and Inclusion Efforts
A large number of women are in the organizing committee, 6 out of 9 members. We also invited and hosted female keynotes and contributed speakers.

Web site: http://cosi.iscb.org/wiki/NetBio:Home

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RegSys: Regulatory and Systems Genomics

The Regulatory and Systems Genomics Community of Special Interest focuses on computational methods that are important in the study of regulation of genes and systems. The RegSys COSI organizes the following activities: (1) ISMB Regulatory Genomics SIG Meeting, (2) RECOMB/ISCB Conference on Regulatory and Systems Genomics and DREAM Challenges, and (3) Top Ten Papers in Regulatory and Systems Genomics.

Leadership Structure
RegSys COSI Steering Committee
Stein Aerts
Jason Ernst (Co-Chair)
Manolis Kellis
Christina Leslie
Saurabh Sinha (Co-Chair, COSI Rep to ISCB Board of Directors)
Lonnie Welch (Co-Chair)
Julia Zeitlinger

ISMB RegSys COSI Organizing Committee

Activities Over the Last Year
The Regulatory and Systems Genomics Community organizes the following activities each year:

1. ISMB Regulatory & Systems Genomics 2-day Track at ISMB

2. RECOMB/ISCB Conference on Regulatory and Systems Genomics and DREAM Challenges

3. Top Ten Papers in Regulatory and Systems Genomics

Equity, Diversification, and Inclusion Efforts
Equity, diversity and inclusion are given careful consideration during selection of chairs and speakers for all events organized by RegSys COSI.

Web site: http://cosi.iscb.org/wiki/RegSIG:Home

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SysMod: Computational Modeling of Biological Systems

The SysMod Community of Special Interests aims at bridging the gap between bioinformatics and systems biology modeling. Recently, aspects of the two fields have converged. Systems modeling has become more reliant on bioinformatic network inference to build models. It has begun to use transcriptomics and proteomics data to train models. Also, more communication between systems modelers and bioinformaticians is needed to build models of whole cells, organs, and organisms. Furthermore, the promises of precision medicine lie, in part, in the interplay between bioinformatics-based analysis of patient data and model-based predictions of treatments.

Leadership Structure
In 2021 Claudine Chaouiya has joined the team of session chairs.

Activities Over the Last Year
The SysMod community is transitioning to become an umbrella organization that integrates more specialized bio-modeling communities. This transition has included co-advertising activities with related gatherings such as the CoLoMoTo Consortium meetings for logical modeling and the Center for Reproducible Biomedical Modeling's online seminars. Further communities of relevance include the COVID-19 Disease Map consortium, the COBRA community, and the COMBINE consortium. A new article about SysMod has been submitted to Bioinformatics at the COSI's fifth anniversary (see the preprint at https://doi.org/10.5281/zenodo.4245269). This article aims to promote interaction among these communities and help the communities recruit researchers to participate in their activities.

The primary activity of SysMod for the past year was the annual meeting at the ISMB conference. Because of the COVID-19 pandemic, the fifth yearly SysMod was held as a virtual meeting. The new format also caused some changes in the structure. This year, SysMod took place over two days. The fewer submissions can be explained by potential insecurity, given the pandemic situation. Some potential authors might not have submitted their work. However, the number of attendance was comparably high as in previous years. The meeting featured three keynote talks, twelve contributed talks, and 14 posters. Throughout the virtual SysMod meeting, Ph.D. students and postdocs lively discussed efforts to integrate further -omics data to improve mechanistic understanding of biological processes. Over the past year, SysMod has also continued to maintain a community discussion list (e.g., the announcement of impactful new research, meetings, job opportunities, etc.) and a community calendar (e.g., conferences, workshops, schools).

Equity, Diversification, and Inclusion Efforts
SysMod aims at inviting a broad diversity of its speakers and participants. Over the years, a balanced representation of ethnicities and genders has brought diverse opinions to the meeting. Further advancing the welcoming culture to all researchers interested in computational systems modeling in biology continues to be an ongoing effort to which the SysMod team is profoundly dedicated.

Web site: https://sysmod.info
Online Community group: https://sysmod.info

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Text Mining for Healthcare and Biology

Text Mining COSI is a community that brings together researchers, computational biologists, bioinformaticians and biomedical text mining specialists seeking to use text mining to advance the biomedical and biological sciences, to bridge the gap between the capabilities of text mining systems and the needs of concrete applications, and to develop new text mining methodologies that advance the state of the art.

Leadership Structure
Organizing Committee:
Robert Leaman, NCBI/NLM/NIH, United States
Lars Juhl Jensen, University of Copenhagen, Denmark
Cecilia Arighi, University of Delaware, United States
Zhiyong Lu, NCBI/NLM/NIH, United States

Steering committee:
Russ Altman, Stanford, USA
Sophia Ananiadou, NaCTem, UK
Alex Bateman, EMBL-EBI, UK
Lynette Hirschman, MITRE Corporation, USA
Larry Hunter, University of Colorado, USA
Alfonso Valencia, BSC-CNS, Spain
Jonathan Wren, Oklahoma Medical Research Foundation, USA
Cathy Wu, University of Delaware, USA

Activities Over the Last Year
- ISMB 2020 text mining track was well attended: 90-110 during keynotes, 50-90 during talks
- Presented a tutorial at ISMB 2020: A practical introduction to biomedical text mining in the era of deep learning. This tutorial covered introductions to biomedical text mining and deep learning, applying deep learning methods to text using word embeddings and state-of-the-art transformer models, common challenges in biomedical text mining, and constructing standard datasets to support further methods improvement.
- The COSI track was centered on applications of text mining. Recurring themes included supporting biocuration, literature indexing and search and pathway construction; other topics included genotype/phenotype associations, using social media and identifying cell types from single cell RNA sequence data
- The COSI track notably included several submissions and the panel discussion addressed several aspects of the COVID-19 pandemic, specifically: recognizing COVID-19-related concepts using weak supervision, exploratory literature search for evidence regarding assertions about COVID-19, extracting information about COVID-19 therapies from the literature, monitoring public sentiment, therapy discussions and misinformation with social media mining, assessing proposed therapies for COVID-19 using machine reading, knowledge extraction and hypothesis evaluation
- COSI track keynote speaker Cathy Wu presented on Collaborative community text mining and semantic computing for biomedical knowledge discovery. Keynote speaker Russ Altman presented on Text mining to understand drug action: from PubMed to Reddit.
- COSI track attendees assembled a collection of resources and tools useful to text mining community for addressing the COVID-19 pandemic

Equity, Diversification, and Inclusion Efforts
We actively sought to achieve gender / ethnic minority diversity in our program, as can be seen in our track statistics.

Web site: http://cosi.iscb.org/wiki/TextMining:Home
Online Community group: https://groups.google.com/g/text-mining-cosi

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TransMed: Translational Medicine Informatics & Applications

Knowledge-based translational medicine is a rapidly growing discipline in biomedical research and aims to expedite the discovery of new diagnostic tools and treatments by using a multi-disciplinary, highly collaborative, "bench-to-bedside" approach. It involves the integration of multiple high dimensional datasets that capture the molecular profiles of patients, as well as detailed clinical information. Within public health, translational medicine is focused on ensuring that proven strategies for disease treatment and prevention are actually implemented within the community, and on progressing towards data-educated personalised therapy. To genuinely realise the promise of Big Data in healthcare, we must consistently collate the data, annotate it with consistent and useful ontologies, apply sophisticated statistical analysis and translate these findings to the clinic. As a community, we will explore the current status of computational biology approaches within the field of clinical and translational medicine. In this COSI we will bring scientists from both academia and industry to exchange knowledge and foster networking, to help in building up of the translational medicine community.

Leadership Structure
Venkata Satagopam is currently the TransMed COSI Representative and a COSI Track Chair. Maria Secrier is currently the alternate COSI Committee Representative, the COSI Proceedings Liaison and a COSI Track Chair. Wei Gu also serves as a COSI Track Chair.

Activities Over the Last Year
The TransMed (https://transmed.github.io/) is an ISMB Community of Special Interest (COSI) that explores the current status of computational biology approaches within the field of clinical and translational medicine. In TransMed meetings, we bring scientists from both academia and industry to exchange knowledge and foster networking, to help in building up of the translational medicine community. The TransMed started as a Special Session at the ISMB/ECCB 2015 and since 2016, it serves as an ISMB COSI, with corresponding Special Interest Group (SIG).

TransMed 2020 meeting was held during the ISMB 2020 virtual conference on July 15, 2020. TransMed COSI 2020 started with a very insightful keynote talk by Prof. Jason H. Moore (Edward Rose, M.D. and Elizabeth Kirk Rose, M.D. Professor, University of Pennsylvania, United States) discussing the 20 Challenges of AI in Medicine. Prof. Moore reviewed and summarised the challenges in (medical) data and machine learning methods and recommended the areas and directions of how these challenges could be tackled in the future. He emphasised that the purpose of discussing these challenges was to raise the awareness and to encourage more research in the area.

The proceedings talks as well as the talks selected from the abstracts covered different methodologies, especially machine learning and their applications in different translational medicine areas including different types of diseases (cancer, Covid-19), seasonal biological patterns, drug response, singling networks, genotype-phenotype associations, pathways and health and lifespan in humans. In total, there were 12 talks and 26 posters

Our COSI session closed with another great keynote talk by Prof. Atul Butte (Priscilla Chan and Mark Zuckerberg Distinguished Professor of Pediatrics, Bioengineering & Therapeutic Sciences, and Epidemiology & Biostatistics at UCSF, United States) on “Precisely Practicing Medicine from 700 Trillion Points of Data”. Prof. Butte highlighted the many freely available data resources currently existing that are still not being exploited to their full potential, including chemical information, clinical trial results and electronic health records. He advocated for the development of methods to effectively mine such datasets to extract clinically meaningful information, and discussed multiple success stories where his initial exploration of the data was converted into multi-million dollar start-ups. The impressive electronic health record database built by his group at UCSF is demonstrating the potential of such resources in predicting disease onset, evolution and outcome. Prof. Butte emphasised the importance of maximising the use of data and technologies beyond scientific publications, and the fact that entrepreneurial initiatives are crucial to drive research endeavours towards societal impact.

Though it was a virtual event, everyone had a wonderful session with existing talks and nice discussions. We also disseminated information via several media channels, including Twitter account (@cosi_transmed) and LinkedIn webpage (Translational Medicine Informatics & Applications Group). Starting from this year, we initiated our TransMed Slack workspace.

Equity, Diversification, and Inclusion Efforts
- We try to have gender and ethnicity balance in the leadership as well as in the selection of invited speakers.

Web site: https://transmed.github.io/
Online Community group: https://twitter.com/cosi_transmed https://www.linkedin.com/groups/8478286/

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VarI: Variant Interpretation

The Variant Interpretation Community of Special Interest (VarI-COSI) is a community of scientists interested in “breaking” the genomic code. The main goal of our COSI is to promote the formation of a collaborative network of scientists interested in the understanding of the meaning of genomic variation as applied to a range of questions, including population studies, functional and evolutionary impacts, and disease.

Leadership Structure
This year Hannah Carter was COSI representative to committee and Antonio Rausell alternate representative. Emidio Capriotti was part of the proceeding committee for the Genomic Variation Analysis track.

Activities Over the Last Year
This year we celebrated the 10th anniversary of the Variant Interpretation community. All the members of the committee started acknowledging Yana Bromberg who significantly contributed to the organization of the meeting since 2011. At VarICOSI 2020, we heard from a fantastic array of speakers on challenges for clinical and evolutionary variant interpretation. Our agenda included three keynote speakers, two proceedings talk, 10 (7 short +3 long) talks from submitted abstracts and a talk from our sponsor, Variantyx.
The VarICOSI was divided into a morning and afternoon session. In the morning session a keynote talk from Kelley Harris presented the results of a study on the mutation rate as a trait in human populations. In the afternoon Lincoln Stein, spoke about novel insights on cancer mutations from the PanCancer study including over 2500 tumor whole genomes. Finally, Fritz Roth described the development and application of Tileseq to systematically probe the landscape of mutations across genetic background and environmental condition. The organizers thank all of our speakers and sponsor for making this another great VarICOSI at ISMB.
The VarICOSI executive committee invited the community to provide feedback regarding meeting content and format, as well as to participate in future sessions of the meeting.

Equity, Diversification, and Inclusion Efforts
The VarI COSI Strongly promotes gender balance. In the past years we had 2 women in the organizing committee. Currently Hannah Carter is our representative to the committee. We alway promote keynotes talk from excellent female scientists.

Web site: http://varicosi.biofold.org/

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