This has been an unusual year, even for ISMB. Due to the worldwide COVID-19 pandemic, the annual ISMB meeting (the 28th Annual Conference on Intelligent Systems for Molecular Biology), initially intended to be held in Montreal, Canada, was instead run as a fully virtual conference on July 13–16, 2020. A huge debt of gratitude is due to International Society for Computational Biology (ISCB) Executive Director Diane Kovats, Director of Conferences Steven Leard and the rest of the conference team for arranging to move the entire meeting online on extremely short notice!
ISMB is the flagship conference of the ISCB and may be considered the world’s premier forum for dissemination of scientific research in computational biology. The Proceedings Track at ISMB provides an opportunity for members of the computational biology research community to submit full length papers featuring original research for thorough review. Both theoretical and applied submissions are welcomed in any field of computational biology; accepted papers appear in this special issue of Bioinformatics and are presented at the conference.
The review process this year was managed by dividing the submitted manuscripts among nine scientific review areas. Program committee recruitment and reviewing were overseen by the Senior Program Committee (SPC), which includes the Proceedings Chairs and the nine sets of Area Chairs (AC), several of whom were nominated by the Communities of Special Interests (COSIs). Reviewers looked for novel, important biological insights; correctness; clarity and potential impact. Once reviews were submitted, papers with discrepant scores were discussed by the reviewers and the relevant ACs, often resulting in refined reviews and scores. Final acceptance decisions were made by the entire SPC, including the Proceedings Chairs listed as authors of this piece, plus the 18 ACs listed in Table 1.
Table 1.
Thematic areas of ISMB2020
| Area | ACs | Submissions | Accepted papers | Acceptance rate (%) |
|---|---|---|---|---|
| Bioinformatics of microbes and microbiomes | Niranjan Nagarajan, Curtis Huttenhower | 21 | 5 | 23.8 |
| Comparative and functional genomics | Carl Kingsford, Shaun Mahony | 43 | 8 | 18.6 |
| Genome privacy and security | Bonnie Berger | 12 | 2 | 16.6 |
| Genomic variation analysis | Tobias Marschall, Emidio Capriotti | 30 | 7 | 23.3 |
| Macromolecular sequence, structure and function | Lenore Cowen, Jérôme Waldispühl | 60 | 14 | 23.3 |
| Population genomics and molecular evolution | Aïda Ouangraoua, Wataru Iwasaki | 16 | 5 | 31.2 |
| Studies of phenotypes and clinical applications | Niko Beerenwinkel, | 65 | 9 | 13.8 |
| Sébastien Lemieux, Teresa Przytycka | ||||
| Systems biology and networks | Sushmita Roy, Mona Singh | 53 | 9 | 16.9 |
| General computational biology | Olga Vitek, Russell Schwartz | 29 | 6 | 20.6 |
Notes: The table lists the ACs for each theme, the number of reviewed papers, the number of accepted papers and the acceptance rate for each area. The special area of General Computational Biology was designated to handle papers on emerging topics or those not fitting in any of the other areas.
Eight of the reviewing areas in Table 1 focused on particular classes of biological problems, some of which are quite broad. The ninth area, General Computational Biology, is intended for submissions on emerging topics or those that do not fit well in other reviewing areas. Some more common topics of manuscripts handled by this area in 2020 included ontologies and bioNLP, single-cell methodologies, CRISPR and imaging applications. Some papers were moved between reviewing areas to avoid conflicts of interest. Abstracts, previously published papers, position papers, perspectives and reviews were not eligible for submission to the ISMB Proceedings track.
In total, 329 manuscripts were submitted and sent out for review. We wish to especially acknowledge all 226 program committee members and 264 sub-reviewers for doing a tough job under adverse circumstances. Many of the world’s initial COVID-19 shutdown periods overlapped with the final weeks of the review period, yet the deadlines for reviewing and decision-making were met. Overall, we received a total of 1078 reviews, with an average of 3.3 reviews per submission. The distribution of the number of reviews per paper is shown in Figure 1.
Fig. 1.
Nearly all manuscripts received at least three reviews; the average was 3.3
Conditional acceptance information was provided to the authors a month after the submission deadline and final acceptance of revised manuscripts was determined a month later. Overall, 65 manuscripts were accepted, for a final acceptance rate of 20%. The distribution of papers reviewed under the different thematic areas is shown in Table 1.
The authors had the opportunity to designate the particular COSI session for which they believed their paper was most suitable. However, many of the submitted manuscripts made no specific COSI session request. Accordingly, accepted papers were first offered to the author-requested COSI if there was one, but the final assignments of accepted papers to COSI sessions were made by the COSI and Proceedings Chairs on the basis of both author and COSI requests. Three papers were assigned to the General Computational Biology session for presentation. The ultimate distribution of accepted papers to COSIs is shown in Table 2.
Table 2.
COSI distribution of accepted ISMB 2020 Proceedings papers
| COSI | Number of papers |
|---|---|
| HiTSeq | 13 |
| NetBio | 7 |
| MLCSB | 6 |
| EvolCompGen | 6 |
| iRNA | 5 |
| 3D-Sig | 3 |
| CAMDA | 3 |
| Function | 3 |
| Microbiome | 3 |
| RegSys | 3 |
| TransMed | 3 |
| General | 3 |
| BioVis | 2 |
| CompMS | 2 |
| VarI | 2 |
| TextMining | 1 |
We are grateful to the ISMB 2020 Steering Committee, Diane Kovats, Steven Leard, Pat Rodenburg and Seth Mulholland for their support, guidance and cheerful handling of both minor logistical questions and big existential ones at this difficult time. Special thanks go also to the SPC, the reviewers and their sub-reviewers, for going above and beyond in maintaining the high standards of ISMB on a time scale that would have been tight even under typical conditions. Thanks to the COSI chairs for great AC nominations, the ACs for being exceptionally responsive and professional and the COSI contacts for additional help during the process of identifying reviewers and in incorporating accepted papers into their programs.
One of the bright spots in recent months has been the way the entire international research community has come together to focus on a common challenge. Data and code sharing have increased, journals have become more willing to consider manuscripts released as preprints, paywalls have been loosened and new collaborations have arisen. We see the ISMB community reflecting these trends, and we are heartened by the hope that some of these moves toward more open science will continue.
Finally, we want to thank everyone who has participated in this conference–from keynote speakers to students attending for the first time. You make this meeting, and the whole ISMB community, what it is. We hereby invite you to read the papers in this Proceedings volume. Have a safe, healthy year and we hope to be able to welcome you in person to ISMB 2021 in Lyon, France.