Leading Professional Society for Computational Biology and Bioinformatics
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ISCB News and Announcements

2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY) In-Person
 

Submit your research to be a part of the 2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY)

 
Abstract Submission Deadline: *October 12, 2021*
Submit your research to be a part of the 2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY)
 
The Rocky 2021 Conference will provide opportunities for short "flash" presentations (10-minute talks) and poster presentations on current projects from as many attendees as possible. Original presentations (including significant works-in-progress) are solicited in all areas that involve the application of advanced computational methods to significant problems in biology or medicine.
 

Registration is OPEN - Join us IN PERSON for Rocky 2021

Registration is OPEN - Join us IN PERSON for Rocky 2021
Conference Dates:  December 2 - 4, 2021
Viceroy Hotel - Snowmass/Aspen, Colorado
Register Today
PLAN AN ACADEMIC RETREAT! Earn a Suite Upgrade AND Free Food or Ski Lift Tickets PLUS one additional student registration at no charge with paid attendance of 10 or more from one school! Click HERE for details.

 ISCBacademy Webinar: COSI Series
 

Exciting October Line-up - Register today for an upcoming ISCBacademy Webinar:

 
Please use the link below to find more information or to register for:
 

October 5, 2021 at 11:00AM EDT - Alternative approach for discovering relationship between bacteriophages and antimicrobial resistance by Roumyana Yordanova, Hokkaido University and Bulgarian Academy of Sciences - Hosted by CAMDA

October 12, 2021 at 11:00AM EDT - Injecting Life into Visualizations for Biomedical Research by Marc Streit, Johannes Kepler University Linz - Hosted by BioVis

October 22, 2021 at 9:00AM UTC - Metabolic modelling of microbial interactions in microbiomes by Aarthi Karthik, Ravikrishnan Raman, and Dinesh Kumar - Hosted by ISCB

To propose a talk for an ISCBacademy Webinar click here.

Register Today!
 

 

 

 International Society for Computational Biology
 
Nominate a Colleague for an ISCB Awards
 

Awards Nominations Deadline - 06 December

Submit your nomination for one of these annual awards today. The program is nomination based and we strong encourage the submission of nominations that are diverse in nature.

The award winners will be announced in Spring 2022.

 
The Overton Prize was established by the ISCB in memory of G. Christian Overton, a major contributor to the field of bioinformatics and a member of the ISCB Board of Directors who died unexpectedly in 2000. The annual prize is awarded for outstanding accomplishment to a scientist in the early to mid-career stage (up to a decade post-degree or equivalent experience*), who has already made a significant contribution to the field of computational biology.
 
ISCB Overton Prize Award
 
 
The Senior Scientist Accomplishment Award recognizes a member of the computational biology community who is more than two decades post-degree (or equivalent experience) and has made major contributions to the field of computational biology.
 
ISCB Accomplishment by a Senior Scientist Award
 
 
The Outstanding Contributions to ISCB Award is in recognition of outstanding service contributions by any member toward the betterment of ISCB through exemplary leadership, education, service, or a combination of the three.
 
 
ISCB Outstanding Contributions to ISCB Award
 
 
The ISCB Innovator Award is given to a leading scientist, 10-20 years post-degree (or equivalent experience*), who consistently makes outstanding contributions to the field of computational biology and continues to forge new directions.
 
ISCB Innovator Award
 

Nominate a Fellow

Fellows Nominations Deadline - 09 December 

The International Society for Computational Biology introduced the ISCB Fellows Program in 2009 to honor members that have distinguished themselves through outstanding contributions to the fields of computational biology and bioinformatics. During the inaugural year of the program, ISCB conferred the Fellow status on the seven winners-to-date of the ISCB Accomplishment by a Senior Scientist Award, and recognized these distinguished scientists during the ISMB/ECCB 2009 conference in Stockholm, Sweden. Since then, ISCB has sought nominations from our community of members, which are reviewed and voted upon by a selection committee. New Fellows are introduced at each year's ISMB conference.

Only members can nominate.

Nominate a Fellow

 

 

 

 

International Society for Computational Biology
ISCB EQUITY DIVERSITY AND INCLUSION  2020-2021 ANNUAL REPORT
ISCB EQUITY DIVERSITY AND INCLUSION 
2020-2021 ANNUAL REPORT
 
Equity, Diversity and Inclusion (EDI) Committee of the International Society for Computational Biology (ISCB)
September 2021
 
Terry Gaasterland (Chair), University of California San Diego, USA, Lucia Peixoto (Chair) Washington State University, USA, Luis Pedro Coelho, Fudan University, China, Casey Greene, University of Colorado School of Medicine, Denver, USA, Priscila Grynberg, MBRAPA, Brazil, Anne-Christin Hauschild, University of Marburg, Germany, Larry Hunter, University of Colorado, Denver, USA, Shirley Liu, Dana Farber Cancer Institute, USA, Tijana Milenkovic, University of Notre Dame, USA, Gonzalo Parra, EMBL, Germany
The International Society for Computational Biology is committed to creating a safe, inclusive, and equal society for all our members. These values are enshrined in the ISCB’s Code of Conduct, values and ethics. We acknowledge, respect, and promote the value of having a diverse community. The ISCB’s Equity, Diversity, and Inclusion (EDI) Committee is an ISCB Outreach Committee and serves the ISCB Board of Directors by considering our shared experiences, and promoting a respectful community that honors the humanity of all. 
 
In principle and in practice, ISCB values and seeks diverse and inclusive participation within the field of computational biology and bioinformatics. ISCB promotes involvement and expanded access to leadership opportunities regardless of race, ethnicity, gender, religion, age, sexual orientation, nationality, disability, appearance, geographic location, or professional level.  ISCB EDI Committee has prepared this annual diversity report which measures the success of diversity promotion within societal activities, specifically leadership, Intelligent Systems for Molecular Biology (ISMB) conference keynote selection, Society’s Awards and election of ISCB Fellows.  The report below details the strategic map for equity, diversity, and inclusion, the tools that have been put in place to support knowledge-building within the area, and where ISCB could improve it’s diversity, equity, and inclusion efforts.   ISCB recognizes that to change the impact of diversity, equity, and inclusion within the field, we ourselves as an organization need to ensure we are equitable and diverse. 
 

SUMMARY OF ISCB EDI RESOURCES INITIATIVES

 
EDI Strategic Plan (2020-2021) 

Components:
  • Initiatives to increase social accountability for change in the ISCB society
  • Obtaining data and developing measures to assess progress
  • Voluntary training: The “ISCB Awareness toolkit”
  • Recruitment initiative
  • Mentoring
Read ISCB’s EDI Strategic Plan
Read ISCB's awareness toolkit associated with the Strategic Plan

EDI Statements and Policies EDI Initiatives 

1.  EDI seminar series

2020-2021: Indigenous Voices in Computational Biology https://www.iscb.org/edi-seminar-series


2.  Women’s history month 2021, daily feature of outstanding women in Computational Biology. 

ANALYSIS OF THE DATA and RECOMMENDATIONS

 
The ISCB Equity, Diversity and Inclusion (EDI) Committee would like to thank the ISCB membership for their participation in the diversity survey of the Society. Your willingness to voluntarily complete this information has given the committee the ability to take a deeper-dive to assess our progress on ensuring equity within the field of Bioinformatics and Computational Biology.   The data presented in this report (as of June 30, 2021) can be viewed in detail at the end of the report.  Based on the survey the ISCB membership is diverse in terms of ethnic origin (53% of those responding are of non-European descent) but heavily male biased. 
 
However, the data presented in this report may not yet accurately capture diversity within ISCB. Response rate on the survey was 75% on gender and 46% on ethnicity. There’s still a substantial number of members that have either not participated in the survey or have preferred not to declare status. We need higher member participation to obtain more accurate data.  The EDI Committee strongly encourages those who have not completed the survey to consider doing so to allow us the ability to make a more accurate analysis. 

ISCB LEADERSHIP & KEYNOTE SPEAKER SELECTION

 
Over the last ten years, ISCB, under the leadership of its presidents and the support of the Executive Committee, Board and membership, has seen significant increases in gender diversity within the leadership of the organization.  When ISCB incorporated in 1997, only two women were representatives on the ISCB Board of Directors. Today, 41% of the ISCB Board of Directors are female and 57% of the Executive Committee (elected officers) are female. Furthermore, 50% of the Committee and Advisory Council Chairs are female and the replacement of retiring/expiring Chairs is conscientiously considered to ensure at minimum gender diversity is achieved within the Committee and Advisory Council leadership.  
 
This conscious effort to ensure gender diversity continued in the selection of keynote speakers for the Intelligent Systems for Molecular Biology (ISMB) conference, ISCB’s flagship and most prestigious conference. 61% of ISMB selected keynote speakers were female between 2016 till present. To further support this initiative, guiding principles for speaker selection were put in place to encourage at least 30% female keynote speakers selection for all ISCB official conferences.  This specific threshold was selected as it represents 5% more than the known male/female breakdown of the professional ISCB membership. 

ISCB AWARDS AND HONORS

 
Whilst the final selection of awardees shows a good gender balance that reflects that of the membership, all ISCB awards and honors, except the service award, show a gender bias during the selection process that is most prominent at the nomination stage. Bias exists regardless of gender of the nominator. We do not know whether this is also true in terms of ethnicity. Given ISCB membership composition and the gender bias reported data, bias in ethnicity of honors is likely. The ISCB committees responsible for the selection of the awards, however, deserve recognition for their clear conscious efforts to ensure at minimum gender diversity at the final selection level, as you see from the data provided. Furthermore, following our review of the election of Fellows, we would also like to highlight the efforts made by the Fellows Committee to ensure the election of a diverse class of Fellows following the 2015 election. New procedures and processes have been put into place to ensure diversity at all levels.   
 
These achievements do not diminish, however, the need to improve the considerable bias at the nominations level.  Steps will be taken to correct this bias. We strongly encourage members to take part in nominating candidates and to use the ISCB awareness toolkit developed by the EDI committee before selecting their candidates. 
 
EDI COMMITTEE RECOMMENDATIONS FOR the ISCB BOARD OF DIRECTORS

1.  A deeper look at the award process is necessary. Some suggestions from the EDI committee to help mitigate bias in the award process:

•  Allow for self-nominations in addition to nominations by others.
•  Make the whole process after the nomination more transparent on the ISCB website, by publicizing the summary statistics both for the nominations and the awards made.
•  Make the award selection committee blind to the initial nomination process to avoid introducing bias based on who the nominator is (or isn’t if we allow self-nominations).
•  If introducing the measures above does not improve bias on awards, consider enforcing a ratio that matches the composition of the society (at the professional level) by the selection committees.

2.   Include completion of the ISCB awareness toolkit in membership profile survey and offer incentives for members to do so (conference ribbons, banners), especially for members that serve on ISCB committees. The fact that the initial nomination stage is where most of the bias is means our community needs to be educated regarding implicit bias.

3.  Our membership is quite diverse in terms of ethnic origin (53% of survey respondents are non-European descent), and many may have limited access to travel to the main conferences based on their location. As meetings go back to in-person, there is an opportunity to leverage our experience over the past year to make sure our meetings are inclusive of our membership. We support ISCB’s goal moving forward to offer as many conferences as financially feasible as hybrid events - in-person and virtual attendance. Conferences that are designed to be hybrid should have live-stream sessions from the conference location, archived recorded sessions that will be accessible to the registered attendance during and after the conference dates, virtual poster presentations and networking opportunities.  We support the continued growth of the ISCBacademy program - webinar series. The revision of our fee structure together with virtual options will ensure a more global and inclusive ISCB community

4.  In the future, we need to collect demographic info for abstract submitters, talk selections, invited talks, etc. for all ISCB-associated conferences. Our initial assessment supports the existence of bias in recognition in our community. Continuing to collect more and better data will help create better strategies on how to address it.

5.  Encourage empirical research into equity, diversity and inclusion in science that utilize rigorous data analysis. Include the following topic on calls for proceedings and abstracts for ISMB.  

Topic title: Equity-focused Research  
Description: This category is for research that examines issues of equity, representation, diversity, or other elements related to datasets, methods, or the field of computational biology at large.  
 
Consider and encourage such submissions also for the journal Bioinformatics Advances.

September 09, 2021:  ISCB Releases Inaugural Equity, Diversity, and Inclusion Report

STATE OF THE SOCIETY - DEMOGRAPHIC DATA

Click here for detailed data
 
 

 

International Society for Computational Biology

In principle and in practice, ISCB values and seeks diverse and inclusive participation within the field of computational biology and bioinformatics. ISCB promotes involvement and access to leadership opportunities regardless of race, ethnicity, gender, religion, age, sexual orientation, nationality, disability, appearance, geographic location, or professional level. As a leading organization in the field of Bioinformatics and Computational Biology, we understand that we have a responsibility to ensure we are promoting diversity within all our programs. ISCB recently conducted an audit (lead by the ISCB Equity, Diversity and Inclusion Committee) of our leadership, awards, Fellows and keynotes, focusing on the time period 2016 – 2021. This time period was selected because it was after the Fellows election in 2015 where ISCB found problems with adequate representation of the diversity of our scientific community in appropriate the election process that the leadership was determined to address. The EDI report is in its final stages and will be released soon.

The Society continues to make progress. We can see that the gender balance in our governance and awards reflect the professional membership of our society. However, problems exist as regards broader diversity. Furthermore, a major finding in the report is the bias that exists within the nomination stage of the ISCB awards and Fellows process. For example, for gender, whereas the M:F ratio for the professional membership is 3:1, the M:F ratio for nominations is 6:1 in some categories. We are determined to address these issues with diversity.

ISCB reminds the community of members that awards and Fellows are selected from nominated candidates.

Without the submission of nominations (or self-nominations starting for awards and Fellows consideration for 2022), the organization cannot improve its diversity among awardees and Fellows.

ISCB strongly encourages this community to read the recently accepted article by ISCB member Casey Greene about our award weaknesses and submit a candidate for consideration that helps us address this weakness.

Thank you in advance for celebrating a colleague of diversity with a nomination.

Annually, ISCB recognizes four scientist through its Awards program, as well as hosts a variety of computational science related competitions.
Self-nominations accepted. Nominations close on December 6th, 2021.

ISCB Overton Prize Award

ISCB Accomplishments by a Senior Scientist

Outstanding Contributions to ISCB Award

ISCB Innovator Award

 
ISCB introduced the ISCB Fellows Program in 2009 to honor members that have distinguished themselves through outstanding contributions to the fields of computational biology and bioinformatics. ISCB seeks nominations from our community of members, which are reviewed and voted upon by a
selection committee. Nominations will close on December 9, 2021.
Submit your nomination today
 
 

 

 

2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY) In-Person

2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY)

In-Person
December 2 - 4, 2021
Viceroy Hotel - Snowmass/Aspen, Colorado
Registration Open

The eighteenth conference is a meeting of the International Society for Computational Biology (ISCB) held each year in Snowmass, Colorado. The Rocky series began nineteen years ago as a regional conference, and has grown into an international program with a spotlight on regional development in the computational biosciences. The presenters of the Rocky conference are early and late career research scientists representing a broad spectrum of universities, industrial enterprises, government laboratories, and medical libraries from around the world.

The conference is a chance to get to know your colleagues near and far, seek collaborative opportunities, and find synergies that can drive our field forward.

The conference includes short "flash" presentations (10 minute talks), poster presentations and keynote presentations on current projects including significant works-in-progress involving the application of advanced computational methods to significant problems in biology or medicine.

The Rocky conference is also a great opportunity for early career researchers to be selected to present their work.  

Check out discounts for groups from one project or institution.  

Visit the website for more information: www.iscb.org/rocky2021

2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY) In-person
 

 ISCBacademy Webinar: COSI Series
 
Register today for the next ISCBacademy Webinar!
 
Please use the link below to find more information or to register for:
 

September 7, 2021 at 11:00 AM EDT - ISCBacademy COSI Series: 3D SIG by Mohammed AlQuraishi, Columbia University - Hosted by 3D SIG

AlphaFold2 burst on the life sciences stage in late 2020 with the remarkable claim that protein structure prediction has been solved. In this talk I will argue that in some fundamental sense the core scientific problem of static structure prediction is finished, but that further maturation is necessary before AlphaFold2 and similar systems can address biological questions beyond those of structure determination itself. I will outline some of these necessary developments and highlight one in particular: the prediction of structure from individual protein sequences. I will describe present challenges and opportunities, and our efforts to tackle them by combining advances in protein language modeling with end-to-end differentiable structure prediction, presenting new results on the prediction of orphan and de novo designed proteins. Time permitting, I will end by speculating on what abundant availability of structural information might mean for the future of biology.

Hosted by:

3D SIG - The International Society for Computational Biology

 
 
Register for an upcoming ISCB Webinar
 

 
International Society for Computational Biology
 

ISCB Announces Results of the
2021 Leadership Elections


 
The Board of Directors of the International Society for Computational Biology (ISCB) is pleased to announce the results of the recent leadership elections.

Members of the society elected the following as Officers beginning January 2022:
 
Officers
Nicola Mulder, Vice President
Janet Kelso, Treasurer
 
Student Council Executive Team
R. Gonzalo Parra, Representative to the ISCB Board of Directors
Handan Melike Dönertaş, Chair
Gabriel Olguin-Orellana,Vice Chair
Ana Castillo Orozco, Secretary 
Yesid Astroz, Treasurer
 

For additional information on ISCB's annual leadership nominations and elections procedures, please see https://www.iscb.org/leadership-nominations-and-elections.

The next call for nominations of directors and officers will open February 2022, for terms beginning January 2023.
 
 
 

 

 

ISMB/ECCB 2021
Day 6, Highlights & Recap!

ISMB/ECCB 2021

 

Day 6: Highlights & Recap!

 

Well that is a wrap! The final day took off and ended with a bang. Today saw a full day of technology with the long awaited Technology Track, the final 7 COSI sessions, and the last Special Session on Single Cell and Spatial Data Analysis.

Highlights
ISCB Accomplishments by a Senior Scientist Award Keynote, Peer Bork gave a the final talk of the conference on Analyzing microbes in us and on our planet. Environmental sequencing, that is metagenomics, has become a major driver for uncovering microbial biodiversity and increasingly also for cataloging molecular functions on our planet. The exponentially increasing metagenomes need computational tools and resources to allow researchers to access and digest these valuable data. Based on methods and resources, developed in their group, but also utilizing public bioinformatics resources, here he introduced into their work on the gut microbiome, aimed at basic understanding, but also at medical applications, showing a few examples from tracing the structure and function of microbiomes in different habitats on earth (ocean and soil) and briefly outlining the concept of interacting computational resources, developed and maintained by a network of researchers across Europe.


 

COSI Recaps

Bioinfo-Core
The Bioinfo-Core COSI session brought together managers and staff working in bioinformatics core facilities around the world. The excellent work done in the following core facilities was presented:

  • Nicole Scherer from the Brazilian National Cancer Institute talked about the hard work and challenges of establishing a core facility from the ground up in a hospital.
  • Gregg TeHennepe from The Jackson Laboratories talked about applying the methods of tools of Agile project management to bioinformatics research support, and presented a case study of a real-life case.
  • Fatima Mitterboeck from Agriculture and Agri-Food Canada presented on the Bioinformatics Research Support Network, community of practice sharing best practices and working towards supporting users at a national scale.
  • Fleur Gahwens presented about building up a bioinformatics community at the Dutch Institute of Ecology, and shared the lessons learned during the development of the epiGBS2 Snakemake-based workflow in that community.
  • Krishna Karuturi from The Jackson Laboratories discussed the comprehensive approach for embracing machine learning and imaging advances in that organization, and the linkages and collaborations required to make that a reality.
  • Ning Zhang from the Stowers Institute presented RiboSeeker, an end-to-end package that integrates a Snakemake workflow and an R package for ribosome profiling.


Our keynote speaker Johannes Köster presented on Snakemake, one of the most widely used and cited workflow management systems. Snakemake's new approaches for modularization and deployment and other new approaches and features were introduced to an audience of nearly 80 attendees.

After the keynote, we had our breakout room discussions where the following topics were discussed:

  1. Workflow managers / pipeline tools
  2. Training
  3. Spatial transcriptomics
  4. Project management
  5. Core facilities during the pandemic and knowledge sharing
  6. Protected data

BOSC
The second and last day of BOSC 2021 started off with a keynote talk by Thomas Hervé Mboa Nkoudou on “Contribution of the maker movement to biotechnology in Africa: An open science perspective”. This is the first BOSC keynote talk that was not given in English: Thomas spoke in his native French, with English subtitles. Thomas emphasized that open source / open data are key to wide dissemination of knowledge in the biosciences and beyond. An example of this openness in practice is the way the Maker movement, which embraces openness, has contributed to the democratization of biotechnology in Africa. Thomas observed that universities have not yet embraced openness and the maker-movement philosophy in African countries; an attendee noted that this is also the case in Europe. Thomas responded that to address this, we need to teach principles, philosophy and give practical experience as early as possible so that new generations consider maker/DIYbio solutions when they are faced with problems themselves.

In the ‘Analysis tools’ session, we heard from David Twesigomwe about a pipeline that incorporates graph based variant calling for Cytochrome genes. Patrick Kunzmann talked about updates to the Python library Biotite that performs sequence and structural analyses. Charlotte Herzeel talked about elPrep, a set of tools that has improved computing performance of popular NGS pipelines. This session also had two talks from the Broad, the first one by Bhanu Gandham on how the GATK pipeline has been adapted to microbes; the final talk was from Michael Gatzen about assessing batch effects for variants generated by two different pipelines.

Workflow Management Systems are always a popular topic at BOSC, and this year was no exception. This session included updates on widely used workflow systems such as Nextflow, Dockstore and Sapporo, and introductions to newer resources such as WARP and WFPM.

A short session on visualization tools and platforms focused on the venerable genome browser, JBrowse, now deployable through Docker and with a major update. It also introduced GO-Figure!, a new viz tool for Gene Ontology terms. The final session of BOSC, Translational Bioinformatics, included hot topics such as knowledge graphs and drug discovery, all in an open source context.

BOSC Chair Nomi Harris ended the day by thanking the many people who helped to make BOSC 2021 possible, including the organizers, reviewers, sponsors, and presenters. We look forward to seeing everyone (hopefully in person) at BOSC 2022!

VarI
VarI COSI’s second day at ISMB ECCB 2021 started with a keynote presentation titled “Mutate everything” by Ben Lehner from the (Centre for Genomic Regulation, Barcelona). Ben presented recent work on mutational scanning of protein coding genes allowing to quantify mutations’ effects on protein folding, binding and aggregation as well as to characterize protein free energy changes for the identification of allosteric sites. Mutational scanning was also a main topic of the round table discussion moderated by Yana Bromberg (Rutger University) with Douglas Fowler (University of Washington), Daniel Gilchrist (NHGRI) and Predrag Radivojac (Northeastern University), where current challenges on variant annotation and interpretation were addressed. Adding to the round table, a total of 7 selected talks were presented with a major focus on clinical interpretation of human variants from sequencing studies, covering a broad range of aspects such as the structural and mutational features of pathogenic variants, the interpretation of Copy Number Variants, and the characterization of gain-of-function variants. The session included a presentation from Variantyx, VarI COSI’s main sponsor, where Alexander Kaplun presented recent computational developments for variant calling in non-uniquely mappable regions from short-read WGS data.

iRNA
The third and last day of the 2021 iRNA COSI had an emphasis on RNA structure/RNA interactions/RNA quantification using long reads and featured two fascinating keynotes. Yue Wan discussed mapping of RNA-RNA interactions with applications illustrated in the analysis of SARS-CoV-2 while Liang Huang talked about the prediction of RNA secondary structure, with interesting historical considerations and comparisons across fields, finishing with the important application of their linear tool to SARS-CoV-2. Contributed talks discussed the transcriptomics analysis of a lncRNA, a snoRNA and a miRNA network as well as important considerations in the analysis of long read and direct RNA sequencing. In addition, the community heard about two challenges started within the context of the RNA society meeting with calls for participation. Overall, the 2021 iRNA COSI was very successful with varied aspects of computational RNA research explored, a timely live panel discussion, fascinating keynotes and enthusiastic poster presentations.

Thank you to our Exhibitors!

 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

See you next year in-person at ISMB 2022!