Meeting Report: BioSharing at ISMB 2010

The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems for Molecular Biology) conference in Boston in 2014. The selected papers span a wide range of topics including the automated re-use and update of ontologies, quality assessment of ontological resources, and the systematic description of phenotype variation, driven by manual, semi- and fully automatic means.

The Intelligent Systems for Molecular Biology (ISMB) conference is the oldest and largest conference that specifically addresses bioinformatics and computational biology, i.e. interdisciplinary research that falls between computer science and biology, ISMB is distinguished from many other conferences in computational biology or artificial intelligence by an insistence that the researchers work with real molecular biology data, not theoretical examples; and from many other biological conferences by providing a forum for technical advances as they occur, which otherwise may be shunned until a firm experimental result is published. The resulting intellectual richness and cross-disciplinary diversity provides an important opportunity for both students and senior researchers. ISMB has become the premier conference series in this field with refereed, published proceedings, establishing an infrastructure to promote the growing body of research. ISMB comprises five main types of presentations: tutorials, plenary presentations, poster presentations, topically focused satellite meetings and software demonstrations. These tutorials and fellows contribute to the development of human resources by allowing students and post-doctoral fellows to reach a state-of-the-art level rapidly, and to begin making contributions to the field. At ISMB 2002, 15 tutorials were held, 50 papers were presented, 498 posters were presented, 6 special interest group meetings here held, and 20 software demonstrations (both non-for-profit and corporate) were presented.

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

The 2009 BioLINK SIG (Special Interest Group) meeting held in Stockholm at the ISMB conference (Intelligent Systems for Molecular Biology—the annual conference of the International Society for Computational Biology) included a new session devoted to the future of scientific publishing. The session was added in response to the very favorable reviews of the 2008 Special Session on the same topic.

COVID-19 in endoscopy: Time to do more?

In this meeting report we give an overview of the talks and presentations from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium held as part of the annual Intelligent Systems for Molecular Biology (ISMB) conference in Toronto, Canada. Furthermore, we detail the role of the Student Council (SC) as an international student body in organizing this symposium series in the context of large, international conferences.

This meeting report gives an overview of the keynote lectures and a selection of the student presentations at the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 8th European Conference on Computational Biology (ECCB). The symposium was held in Stockholm, Sweden from June 27 to July 2, 2009. We also report on other Student Council events that were organized at ISMB/ECCB 2009.

<em> Every summer we celebrate our birthday at the ISMB (Intelligent Systems for Molecular Biology) conference, and this was a particularly memorable and important one – being the 5 <sup> th </sup> birthday of GigaScience, and 25 <sup> th </sup> edition of the ISMB. </em>

Each year, the International Society for Computational Biology (ISCB; http://www.iscb.org) makes awards for exceptional achievement to two scientists. The ISCB Accomplishment by a Senior Scientist Award honours career achievement in recognition of distinguished contributions over many years in research, teaching, service, or any combination of the three. In 2012 this award is going to Gunnar von Heijne of the Stockholm University in Sweden. The Overton Prize recognizes a young scientist in the early to mid-stage of his or her career who has already achieved a significant and lasting impact in the field of computational biology. In 2012, the Overton Prize is being awarded to Ziv Bar-Joseph of Carnegie Mellon University in Pittsburgh, Pennsylvania, United States. The recipients were chosen by the ISCB's awards committee chaired by Alfonso Valencia at the CNIO (Spanish National Cancer Research Centre) in Madrid. The winners will receive their awards at the ISCB's annual Intelligent Systems for Molecular Biology (ISMB) meeting, where they will deliver keynote talks. ISMB 2012 (http://www.iscb.org/ismb2012) marks the 20th anniversary of the conference, and will take place July 15–17 in Long Beach, California, United States.

The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML). The LTER is one of the top National Science Foundation (NSF) programs in biology since 1980, representing diverse ecosystems and creating long-term, interdisciplinary research, synthesis of information, and theory. The adoption of EML as the LTER network standard has been key to build network synthesis architectures based on high-quality standardized metadata. EML is the NSF-recognized metadata standard for LTER, and EML is a criteria used to review the LTER program progress. At the workshop, a potential crosswalk between the GCDML and EML was explored. Also, collaboration between the LTER and GSC developers was proposed to join efforts toward a common metadata cataloging designer's tool. The community adoption success of a metadata standard depends, among other factors, on the tools and trainings developed to use the standard. LTER's experience in embracing EML may help GSC to achieve similar success. A possible collaboration between LTER and GSC to provide training opportunities for GCDML and the associated tools is being explored. Finally, LTER is investigating EML enhancements to better accommodate genomics data, possibly integrating the GCDML schema into EML. All these action items have been accepted by the LTER contingent, and further collaboration between the GSC and LTER is expected.

Discovering the intelligence in molecular biology

This is the slide deck for the talk given by Bhavesh Patel at the Bioinformatics Open Source Conference (BOSC) 2024 conference, part of the International Conference on Intelligent Systems for Molecular Biology ( ISMB ) held in Montreal, Canada. Details about the conference are available at https://www.open-bio.org/events/bosc-2024. The talk instroduced Codefair, an open source and free GitHub app for making biomedical research software FAIR. Abstract: Abstract: We present Codefair, an innovative solution that helps researchers make their biomedical research software Findable, Accessible, Interoperable, and Reusable (FAIR), i.e. optimally reusable by humans and machines. The FAIR Biomedical Research Software (FAIR-BioRS) guidelines provide actionable instructions for making biomedical research software FAIR. While designed to be convenient to follow, we learned that their implementation can still be time consuming for researchers. To address this challenge, we are developing Codefair, a free and open source GitHub app that acts as a personal assistant for making research software FAIR. Researchers simply need to install Codefair from the GitHub marketplace and proceed with their software development as usual. By leveraging GitHub’s tools such as Probot, Codefair monitors activities on the software repository, communicates via GitHub issues, and submits pull requests to help researchers make their software FAIR. Currently, Codefair helps with including essential metadata elements such as license file, CITATION.cff metadata file, and codemeta.json metadata file. Additional features are being added to provide support for complying with best coding practices, archiving on Zenodo, registering on bio.tools, and much more to cover all the steps for making software FAIR. By alleviating their burden in the process, we believe Codefair will empower and encourage biomedical researchers into adopting FAIR and open practices for their research software. We present here our approach to developing Codefair, highlight the current and planned features, and explain how the community can benefit from and contribute to Codefair.

SummaryThe Computational Modelling of Systems Biology (SysMod) Community of Special Interest (COSI) convenes annually at the Intelligent Systems for Molecular Biology (ISMB) conference to facilitate knowledge dissemination and exchange of research findings on systems modelling from interdisciplinary domains. The SysMod meeting 2022 was held in a hybrid mode in Madison, Wisconsin, spanning a 1-day duration centred on modelling techniques, applications, and single-cell technology implementations. The meeting showcased innovative approaches to modelling biological systems using cell-specific and multiscale modelling, multiomics data integration, and novel tools to develop systems models using single-cell and multiomics technology. The meeting also recognized outstanding research by awarding the three best posters. This report summarizes the key highlights and outcomes of the meeting.Availability and implementationAll resources and further information are freely accessible at https://sysmod.info.

Birthdays, <strong> BOSC, Beatles and Bioinformatics with a Merseybeat </strong> Conference season is upon us, and the <em> GigaScience </em> team have just returned from a magical mystery tour to Liverpool. Regular readers will know <em> GigaScience </em> launched at the ISMB (International Conference on Intelligent Systems for Molecular Biology) in 2012, and every year we attend and celebrate our birthday at the meeting.

This presentation was part of the ELIXIR Special Track at the joint 25th Annual International Conference on Intelligent Systems for Molecular Biology and the 16th European Conference for Computational Biology (ISMB/ECCB) on 25 July 2017. ELIXIR Track one showcased to delegates the activities and outputs of ELIXIR’s five Platforms (Tools, Data, Interoperability, Compute and Training). Through talks from ELIXIR partners and interactive discussions, delegates saw the services and resources made available via ELIXIR, and how they could engage in and contribute to their development. ELIXIR Track two followed a similar format and showcased the outputs of ELIXIR’s Use Cases (Marine Metagenomics, Plant Sciences, Rare Diseases and Human Data), the Capacity Building programme and Industry Engagement.