ISCB Announces Results of the
2021 Leadership Elections

ISMB/ECCB 2021
Day 6, Highlights & Recap!

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.

ISMB/ECCB 2021
Day 6 - Conference Highlights & Things to Know

Friday, July 30: Highlights & Reminders

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

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

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.

ISMB/ECCB 2021
Day 5, Highlights & Recap!

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.

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

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

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