Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.

Abstract

Not specified

Authors: M. Golebiewski, G. Bader, P. Gleeson, T. E. Gorochowski, S. M. Keating, M. Konig, C. J. Myers, D. P. Nickerson, B. Sommer, D. Waltemath, F. Schreiber

Date Published: 1st Mar 2024

Publication Type: Journal

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

Abstract (Expand)

INTRODUCTION: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing … SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. METHODS: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. RESULTS: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. DISCUSSION: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.

Authors: A. Niarakis, M. Ostaszewski, A. Mazein, I. Kuperstein, M. Kutmon, M. E. Gillespie, A. Funahashi, M. L. Acencio, A. Hemedan, M. Aichem, K. Klein, T. Czauderna, F. Burtscher, T. G. Yamada, Y. Hiki, N. F. Hiroi, F. Hu, N. Pham, F. Ehrhart, E. L. Willighagen, A. Valdeolivas, A. Dugourd, F. Messina, M. Esteban-Medina, M. Pena-Chilet, K. Rian, S. Soliman, S. S. Aghamiri, B. L. Puniya, A. Naldi, T. Helikar, V. Singh, M. F. Fernandez, V. Bermudez, E. Tsirvouli, A. Montagud, V. Noel, M. Ponce-de-Leon, D. Maier, A. Bauch, B. M. Gyori, J. A. Bachman, A. Luna, J. Pinero, L. I. Furlong, I. Balaur, A. Rougny, Y. Jarosz, R. W. Overall, R. Phair, L. Perfetto, L. Matthews, D. A. B. Rex, M. Orlic-Milacic, L. C. M. Gomez, B. De Meulder, J. M. Ravel, B. Jassal, V. Satagopam, G. Wu, M. Golebiewski, P. Gawron, L. Calzone, J. S. Beckmann, C. T. Evelo, P. D'Eustachio, F. Schreiber, J. Saez-Rodriguez, J. Dopazo, M. Kuiper, A. Valencia, O. Wolkenhauer, H. Kitano, E. Barillot, C. Auffray, R. Balling, R. Schneider

Date Published: 29th Feb 2024

Publication Type: Journal

Data Formats for Systems Biology, Systems Medicine and Computational Modeling

Abstract (Expand)

In systems biology and systems medicine data of many different types and obtained from manifold methods are used to set up computational models for simulations and predictions. These data need to be … interoperable to integrate them into the models or use them for model validation. To achieve this, standards are crucial for structuring, describing, and associating models and data, as well as their respective parts, graphical visualization, and information about applied experimental or computational methods. Such standards also assist with describing how constituent parts interact together, or are linked, and how they are embedded in their environmental and experimental context.

Authors: Martin Golebiewski, Gerhard Mayer

Date Published: 2024

Publication Type: InCollection

Data Formats for Systems Biology and Quantitative Modeling

Abstract (Expand)

Data standards support the reliable exchange of information, the interoperability of tools, and the reproducibility of scientific results. In systems biology standards are agreed ways of structuring, … describing, and associating models and data, as well as their respective parts, graphical visualization, and information about applied experimental or computational methods. Such standards also assist with describing how constituent parts interact together, or are linked, and how they are embedded in their environmental and experimental context. Here the focus will be on standards for formatting models and their content, and on metadata checklists and ontologies that support modeling.

Author: Martin Golebiewski

Date Published: 2019

Publication Type: Journal

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

Abstract (Expand)

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together … researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers

Date Published: 24th Aug 2020

Publication Type: Journal

Proceedings of the 10th Computational Modeling in Biology Network (COMBINE) Meeting 2019

Abstract (Expand)

These are the conference proceedings of COMBINE 2019, the 10th Computational Modeling in Biology Network (COMBINE) meeting that took place in Heidelberg (Germany) from July 15th to July 19th, 2019. The …e Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models in the life sciences. It was created in 2010 to enable the sharing of resources, tools, and other infrastructure, and to coordinate standardization efforts for modeling in biology. COMBINE brings standard communities together around activities that are mutually beneficial. These activities include making specification documents available from a common location, providing a central point of contact, and organizing regular face-to-face meetings. To this end, the COMBINE network organizes an annual conference style meeting (the COMBINE Forum) and annual hackathon style events called HARMONY (Hackathon on Resources for Modeling in Biology), as well as tutorials and training events. At COMBINE 2019 a combination of keynote lectures, invited talks and interactive breakout discussions, as well as contributed talks, posters and lightning talks, selected from submitted abstracts, provided the basis for the meeting, offering diverse formats to exchange information, to discuss and work on interoperability problems and to demonstrate support for standards implemented in modelling tools, platforms and databases. One special focus of COMBINE 2019 was on the standardization need in systems medicine, which has been recognized as a necessity for computer-assisted personalized medicine. To direct attention to this topic, the European standardization framework for data integration and data-driven in silico models (EUSTANDS4PM) organized a workshop as part of COMBINE 2019. Also, reproducibility in modelling was a main topic, as reflected by several sessions and workshops. Besides these focus themes, also sessions, workshops and breakout discussions around single standards, their further development and their interoperability helped to advance the standardization, standing in the tradition of COMBINE.

Authors: Martin Golebiewski, Dagmar Waltemath

Date Published: 15th Jul 2019

Publication Type: Proceedings

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