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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.
 
 
 

 

 

International Society for Computational Biology
 
Final days to submit your nomination for ISCB Board of Director Positions!  
 
ISCB Board of Directors Nominations Deadline: April 15, 2021
The Nomination Period for ISCB Officers and Board of Directors is Open!
ISCB Officer Nominations Deadline: June 10, 2021

ISCB is encouraging members to submit nominations for the Society’s leadership - Board of Directors and open Officer positions.  Nominations are submitted at www.iscb.org/nominate (you must login to your membership record to access the nomination form). In all cases, self-nominations will not be accepted.

The 2021 Officer positions to be elected are Treasurer and Vice President.  If you know of excellent candidates that meet the eligibility requirements, please be sure to submit your nomination(s). Details of the positions, procedures, requirements, and timeline are available on the ISCB website at: www.iscb.org/leadership-nominations-and-elections.

We are looking forward to an active participation by the ISCB membership in the nomination and election process, and we thank you in advance for your qualified nominations.

If you have any questions, please reach out to This email address is being protected from spambots. You need JavaScript enabled to view it..

 

 

 

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!

 

 
 

 
 

ISMB/ECCB 2021
Day 5, Highlights & Recap!

ISMB/ECCB 2021

 

Day 5: Highlights & Recap!

 

With only one day left, ISMB/ECCB 2021 gave us a day starting off with Exhibitor Demos from EMBL-EBI, PerMedCoE, and GOBLET. The day continued into 9 different COSI tracks, including one for General Computational Biology, and a Special Session Final Project Presentations: Collaborative Tools for Protein Analysis Hackathon 2021.

Highlights
ISCB Innovator Award Keynote, Ben Raphael gave an engaging talk on Quantifying Tumor Heterogeneity across Time and Space. Tumors are heterogeneous mixtures of normal and cancerous cells with distinct genetic and transcriptional profiles. In this talk, he presented present several computational approaches to quantify tumor heterogeneity and to study tumor evolution using single-cell and spatial sequencing technologies. For single-cell DNA sequencing data, he described algorithms to reconstruct tumor evolution from multiple types of somatic mutations and how to use these approaches to analyze changes in tumor genomes over time. For spatial transcriptomics data, he introduced algorithms to detect genomic aberrations and to align and integrate data from multiple adjacent tissue sections leveraging both spatial and transcriptional similarity. The applications of these methods to quantify spatial heterogeneity in several cancer types were illustrated.



 

*Live sessions will be posted within 24 to 48 hours for rendering & editing. Please make sure to check back for the recordings and to keep the conversations going*


COSI Recaps

BOSC

BOSC 2021 (https://www.open-bio.org/events/bosc-2021/), the 22nd annual Bioinformatics Open Source Conference, kicked off this morning with opening remarks by BOSC Chair Nomi Harris, speaking from her home in California at 4:00am local time. The opening session also included an overview of the Open Bioinformatics Foundation by OBF President Peter Cock.

The first BOSC 2021 keynote talk, “Significant heterogeneities: Ecology’s emergence as open and synthetic science”, was delivered live by Christie Bahlai. Ecology has not been a big topic at past BOSCs, but Christie’s approach to open and inclusive science strongly resonated with our community. One attendee commented, “Christie Bahlai's keynote was inspiring and a breath of fresh air. +1 to calling out open science purists and the call for collective responsibility.”

Christie’s keynote was followed by a session on Standards and Practices for Open Science. One speaker in that session, Dhrithi Deshpande, spoke about the disappointingly low percentage of scientific papers that provide a link to the code (only about 12% -- though up from only 1% in 2016!), and noted that articles that share code tend to get cited more.

The next session, Tools for Open Science, started off with a well-received talk by Thorin Tabor about GenePattern, a reproducible research platform built on top of Jupyter Notebook.

Today’s final BOSC session was a joint session with Function COSI, chaired by Iddo Friedberg, featuring a keynote talk by Lara Mangravite on “Open approaches to advance data-intensive biomedicine.” 210 participants attended this joint session. Lara noted that clinical applications need access to high-quality data, but broad accessibility of human clinical data is difficult due to privacy issues, and access to analysis capabilities is distributed inequitably and tends to leave out those in the global south. Lara discussed some possible mitigations for those challenges.

Birds of a Feather, which bring together participants to chat informally about a shared interest, are always a popular feature of ISMB. In the BoF “Next steps for computational reproducibility toward fully executable papers”, there were discussions around ‘What is reproducibility?” and how do we incentivize new PIs to make reproducible work? Some cloud frameworks like Terra allow for reproducibility and lower the barrier for those who don’t have computational infrastructure in house. On the other hand, what about cloud costs? And is the reason why more papers aren’t reproducible the lack of skilled software engineers on the team?

The day ended with a hangout in the BOSC roundtable (which quickly ran into the 16-person maximum) that evolved into a discussion of the OBF and new ways for it to serve the open source bioinformatics community.

Don’t miss the second and final day of BOSC 2021 tomorrow, which begins with the last of our three keynotes, Thomas Hervé Mboa Nkoudou speaking about “Contribution of the maker movement to biotechnology in Africa: An open science perspective” (in French with English subtitles).

CAMDA

The 2nd day of virtual CAMDA 2021 started with an exceptional talk by Weida Tong, director of the Division of Bioinformatics and Biostatistics at the NCTR of the US FDA. Dr Tong discussed five common myths about AI and their implications for regulatory science, and provided a broad overview of how the FDA uses AI/ML techniques in support of the prediction of Drug Induced Liver Injury (DILI). This was followed by further presentations employing a variety of AI language models to identifying scientific papers relevant to drug induced liver injury, as benchmarked by a CAMDA challenge organized jointly with the US FDA with support of IARAI Vienna. The seond half of the day was devoted to the Metagenomic Phage Forensics of Anti-Microbial Resistance challenge based on recently published MetaSUB Consortium data, which was explored by the CAMDA community this year for the first time, yielding novel complex relationships between phages and AMR that indicated a new for further investigations. The rich world of modern meta genomic data was then brilliantly characterised in our keynote by Nikos Kyrpides from the DOE Joint Genome Institute, ranging from the Earth microbiome to the Global virome.

Join us on Friday for an introduction to Disease Maps for modelling COVID-19 by Maria Peña Chilet of the FPS in Seville, followed by contributed talks of the matching data analysis challenge. In the next session we host ISMB/ECCB proceedings presentations on using AI/ML in cancer studies as well as AI-driven Cloud Laboratories. We will wrap up the day with the CAMDA Cafe where the CAMDA community will discuss the Grand challenges of our times to tackle in the coming years, and finishing with the awards ceremony for the traditional CAMDA Trophy for the best presentation. Join us! See www.camda.info for details.

iRNA
The second day of the iRNA COSI 2021 was dominated by epitranscriptomics. The keynote was given by Kathi Zarnack from the Buchmann Institute for Molecular Life Sciences in Germany who discussed the detection/prediction of m6A RNA modifications using transcriptomics data and machine learning, identifying sites within consensus DRACH motifs but also others, providing a rich resource for further studies. Two contributed talks on splicing kinetics and modeling of multivalent binding by RNA-binding proteins were followed by five talks on RNA modification detection from sequencing, raising important common issues and challenges which were addressed in our live panel discussion, to which participated Nicole Martinez, Shengdong Ke and Schraga Schwartz. The panel highlighted the fact that while a decade ago, the challenge in epitranscriptomics was to determine where the modifications are, with rapid and considerable increases in technology capacity brought on by innovations in the field, we are now switching gears and focusing on questions like the function of the modifications, how to address the interconnectedness of the process and the effects throughout the life cycle of the targeted RNA, and the use of systematic perturbations and their analysis using machine learning to understand what the modifications are really doing in the cell. Our panel was followed by our second poster session and our traditional social time with quiz during which we took time to catch up and learned much trivia about the Olympics including surprising facts.

VarI
During the first day of the VarI meeting we had two keynote talks. Alessandra Carbone (Sorbonne University) presented her recent work on the analysis of evolutionary information for detecting protein sites in viral proteomes important for protein-protein interaction and drug resistance. Later, Ben Langmead (John Hopkins University) presented methods for reducing reference bias in the detection of human variations. The proposed approaches are based on new algorithms that allow to align sequencing reads to the reference genome of different populations. The VarI meeting also hosted a proceeding talk from Chirag Jain who presented a new approach for minimizing variation graph size that allows to reduce the computational complexity in the methods for reducing genome bias. In the first days the program included 6 selected presentations focusing on variant prioritization, sex dependent genotype association studies and pleiotropy. Finally, we had a poster session with 18 works presented.

Tomorrow we will have a keynote talk from Ben Lehner (Centre for Genomic Regulation) and a roundtable discussion with Yana Bromberg, (Rutger University), Douglas Fowler (University of Washington), Daniel Gilchrist (NHGRI) and Predrag Radivojac (Northeastern University). Alex Kaplun will present the research activity of Variantyx which has been our main sponsor in the last few years.

Exhibitor Spotlight:



PerMedCoE Demo Presentations:

Track Content:
A Roadmap to Scalability in Personalised Medicine, by José Carbonell
HPC-enabled multiscale simulation to uncover mechanistic insights in the COVID-19 infection
PerMedCoE Building Blocks, by Henrik Nortamo
PerMedCoE Building Blocks & Workflows design, by Javier Conejero
PhysiCell-MPI / PhysiCell-X, by Gaurav Saxena
Multiscale modeling with PhysiBoSS, by Vincent Noël
COBREXA.jl: Metabolic Modeling on HPC, by Miroslav Kratochvil
CellNOpt / CARNIVAL, by Bartosz Bartmanski
The PerMedCoE Competency Framework, by Marta Lloret-Llinares
PerMedCoE Training Activities, by Daniel Thomas López

EMBL-EBI Demo Presentations:
Track Content:
Bioinformatics training: Curated course collections and new training materials
New EMBL-EBI training website and upgraded online tutorials

 
Start your morning off right and head over to the Expo Showcase for the Exhibitor Demos. Grab some coffee and get ready to learn and discover.
 

Don't Forget to Visit Our Exhibitors!

 
 
Career Center and Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the Conference Jobs Board located at:
https://www.iscb.org/cms_addon/conferences/ismbeccb2021/jobpost/jobs/jobs.php
 
 

Cheat-Sheet Section/Platform Tips:
From time to time we may experience technical issues. When in doubt, give the system a quick refresh!

Updating the Time zone
The ISMB/ECCB 2021 virtual platform is enabled with time zone localization to enhance usability. In order to set the platform to your local time zone, click on "Full schedule" and then click on the dark grey "My Time Zone" box to ensure it is activated. Once clicked, the box will darken in color and your schedule will automatically be viewed in your local time zone.

Struggling with UTC conversion - UK +1 CEST +2 EDT -4, CDT -5, MDT -6, PDT -7, AEST +10, Tokyo +9, Beijing +8

Roundtables
Don't forget you can video-chat & network with up to 15 people at the Café Connect “Roundtables” (https://ismbeccb2021.showcare.io/roundtables/).

*Roundtables are pre set up for each COSI (including BOSC), and you can also create your own roundtable!
 
Navigating the Platform
The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.

 

Miss a talk? Watch it On-Demand!
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recordings
• The virtual platform and content will be available to attendees following the conference until November 30, 2021.

 

Tomorrow, Friday, July 30: Highlights & Reminders

HAPPY LAST DAY! Don't forget to pop over to the Research Exchange Forum and pay a visit to our amazing Exhibitors!
 
11:00 UTC: COSI Tracks: MLCSB, CAMDA, BioInfo Core, VarI, BOSC, SysMod, iRNA
11:00 UTC: Covid-19 Special Track & Panel: This panel will compare different models to access, share and protect COVID-19 data, evaluate their advantages, limitations and complementarity to prevent and control pandemics.
11:00 UTC: Special Session: Single Cell and Spatial Data Analysis
11:00 UTC: Technology Track:

11:00-11:20
Phyre2 and Missense3D: Protein structure prediction and missense variant analysis
11:20-11:40
Using CATH-Gene3D v4.3 and its resources to predict the structure and function of novel protein sequences
11:40-12:00
DeepChain: A platform for protein design
12:00-12:20
Developing a reusable and versatile virtual bioinformatics training platform in the de.NBI cloud
12:40-13:00
The EMBL-EBI search and sequence analysis tools APIs and their role during the current COVID-19 pandemic
13:00-13:20
The European COVID-19 Data Portal – Accelerating COVID-19 Research through Open Data Sharing
13:20-14:00
PerMedCoE: A roadmap to scalability in Personalized Medicine
14:20-14:40
The GenePattern Notebook Environment
14:40-15:20
Integrated Pathway/Genome/Omics Informatics in Pathway Tools and BioCyc GenePattern Notebook Environment

   
15:20 UTC: ISCB Accomplishments by a Senior Scientist Award Keynote:  Peer Bork

16:20 UTC:   Awards and Closing Ceremony 
 
 
Anyone else sneaking in some Olympics viewing between the #ISMB/ECCB21 sessions?  Share your best scientific session/Olympic viewing set up from this week and don't forget to tag the Conference! 
 
 
Cast Your Ballot!
Members!! Make your voice heard - Cast your ballot today!
 
ISCB Election - Polls are Open
 
 
 
 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Day 1, Highlights & Recap!

ISMB/ECCB 2021

 

Day 1: Highlights & Recap!

 

Thank you to everyone for joining ISMB/ECCB 2021 from all over the world and sticking with us through some technical issues.   We hope you found the first day full of innovation, stellar science and amazing opportunities!  See you tomorrow for another engaging and smoother day!

Highlights
ISMB/ECCB 2021 began its 20th joint conference with an intense line up of sessions.  The first day culminated in the first live Poster Session and an interesting keynote address on Phylogenomics and Systems Biology approaches reveal conserved adaptive processes in Atacama Desert plants by the distinguished keynote Rodrigo A. Gutierrez. 


Cheat-Sheet Section/Platform Tips:
From time to time we may experience technical issues.  When in doubt, give the system a quick refresh!


Miss a talk?
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recording

SPEAKERS: remember you can continue the conversation in Cafe Connect!  

*Live presentations such as COSI keynote talks, panels, and the Distinguished Keynotes are being processed and may take up to 48 hours to fully post.

Cast Your Ballot!
Members!!  Make your voice heard - Cast your ballot today!
 
ISCB Election - Polls are Open
 
 

Tomorrow, Monday, July 26: Highlights & Reminders

10:00 UTC: ISCB Town Hall Meeting (LIVE)
11:00 UTC: COSI Tracks: HitSeq, 3Dsig, CompMS, EvolCompGen,
Education, RegSys, BioVis, TransMed, Bio-Ont, NetBio
15:20 UTC: Research Exchange Forum includes Posters and Exhibitors / BoFs
15:20 UTC: 
Exhibitor Demos: PerMedCoE, EMBL-EBI, GOBLET, EMBL-EBI, de.NBI
16:20 UTC ISCB Overton Prize Keynote: Barbara Engelhardt
17:20 UTC:
Daily Closing Comments
 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics