Falk Schreiber

About Falk Schreiber:
No description specified

SEEK ID: https://fairdomhub.org/people/1533

Location:  Germany

ORCID: Not specified

Joined: 3rd Apr 2020

Expertise: Bioinformatics, Systems Biology, dynamics of biological networks, Software Engineering, SBGN, Visualisation, Immersive Analytics, Network Analysis, Metabolic Networks, Collective Behaviour, Mechanistic Modelling

Tools: VANTED, SBGN-ED, MetaCrop, TEAMwISE

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Project positions

COVID-19 Disease Map (Universität Konstanz)

Related items

Disease Maps

The Disease Maps Project is designed as a large-scale community effort. It is a network of groups that work together in order to better understand disease mechanisms. The project exchanges best practices, share information, develop tools to make it easier for all the involved groups to achieve their goals.

Projects: COVID-19 Disease Map

Web page: https://disease-maps.org

COVID-19 Disease Map

Here we share resources and best practices to develop a disease map for COVID-19. The project is progressing as a broad community-driven effort. We aim to establish a knowledge repository on virus-host interaction mechanisms specific to the SARS-CoV-2. The COVID-19 Disease Map is an assembly of molecular interaction diagrams established based on literature evidence.

Programme: Disease Maps

Public web page: http://doi.org/10.17881/covid19-disease-map

Universität Konstanz

Country:  Germany

City: Konstanz

Web page: https://www.uni-konstanz.de/en/

Graphical exploration and topological analysis
COVID-19 Disease Map

We performed topological analysis on the diagrams of the COVID-19 DM repository using the tool Vanted / SBGN-ED, which supports the import and export of several standard formats (such as SBML, SBGN-ML, and GML).

Submitter: Felicia Burtscher

Studies: Topological analysis of individual pathway networks and aggregated netwo...

Assays: No Assays

Topological analysis of individual pathway networks and aggregated network with LMME-DM
COVID-19 Disease Map

To allow detailed visual analysis of the overall system and its parts, we used a customised version of our Vanted extension LMME (Large Metabolic Model Explorer) to construct an overview graph, showing one node per pathway and the respective interconnecting species. We performed a comprehensive analysis of node centralities on two levels: on the level of the individual pathway networks as well as on the level of an aggregated network which is composed of the individual networks. This allows ...

Submitter: Felicia Burtscher

Investigation: Graphical exploration and topological analysis

Assays: No Assays

RTC and transcription (COVID-19 Disease Map)
COVID-19 Disease Map

Pathway: Assembly of the Replication Transcription Complex and Transcription

Creators: Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber

Submitter: Marek Ostaszewski

External Link
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
COVID-19 Disease Map

Abstract (Expand)

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets … of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

Authors: M. Ostaszewski, A. Niarakis, A. Mazein, I. Kuperstein, R. Phair, A. Orta-Resendiz, V. Singh, S. S. Aghamiri, M. L. Acencio, E. Glaab, A. Ruepp, G. Fobo, C. Montrone, B. Brauner, G. Frishman, L. C. Monraz Gomez, J. Somers, M. Hoch, S. Kumar Gupta, J. Scheel, H. Borlinghaus, T. Czauderna, F. Schreiber, A. Montagud, M. Ponce de Leon, A. Funahashi, Y. Hiki, N. Hiroi, T. G. Yamada, A. Drager, A. Renz, M. Naveez, Z. Bocskei, F. Messina, D. Bornigen, L. Fergusson, M. Conti, M. Rameil, V. Nakonecnij, J. Vanhoefer, L. Schmiester, M. Wang, E. E. Ackerman, J. E. Shoemaker, J. Zucker, K. Oxford, J. Teuton, E. Kocakaya, G. Y. Summak, K. Hanspers, M. Kutmon, S. Coort, L. Eijssen, F. Ehrhart, D. A. B. Rex, D. Slenter, M. Martens, N. Pham, R. Haw, B. Jassal, L. Matthews, M. Orlic-Milacic, A. Senff Ribeiro, K. Rothfels, V. Shamovsky, R. Stephan, C. Sevilla, T. Varusai, J. M. Ravel, R. Fraser, V. Ortseifen, S. Marchesi, P. Gawron, E. Smula, L. Heirendt, V. Satagopam, G. Wu, A. Riutta, M. Golebiewski, S. Owen, C. Goble, X. Hu, R. W. Overall, D. Maier, A. Bauch, B. M. Gyori, J. A. Bachman, C. Vega, V. Groues, M. Vazquez, P. Porras, L. Licata, M. Iannuccelli, F. Sacco, A. Nesterova, A. Yuryev, A. de Waard, D. Turei, A. Luna, O. Babur, S. Soliman, A. Valdeolivas, M. Esteban-Medina, M. Pena-Chilet, K. Rian, T. Helikar, B. L. Puniya, D. Modos, A. Treveil, M. Olbei, B. De Meulder, S. Ballereau, A. Dugourd, A. Naldi, V. Noel, L. Calzone, C. Sander, E. Demir, T. Korcsmaros, T. C. Freeman, F. Auge, J. S. Beckmann, J. Hasenauer, O. Wolkenhauer, E. L. Wilighagen, A. R. Pico, C. T. Evelo, M. E. Gillespie, L. D. Stein, H. Hermjakob, P. D'Eustachio, J. Saez-Rodriguez, J. Dopazo, A. Valencia, H. Kitano, E. Barillot, C. Auffray, R. Balling, R. Schneider

Date Published: 19th Oct 2021

Publication Type: Journal

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
COVID-19 Disease Map

Abstract

Not specified

Authors: Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta‐Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic‐Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean‐Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban‐Medina, Maria Peña‐Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Wilighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez‐Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider

Date Published: 1st Oct 2021

Publication Type: Journal

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map

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: 29th Jun 2020

Publication Type: Journal

Specifications of standards in systems and synthetic biology: status and developments in 2020
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology. …Not specified

Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 29th Jun 2020

Publication Type: Journal

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational … modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

Authors: Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 13th Jul 2019

Publication Type: Journal

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), FAIRDOM & LiSyM & de.NBI Data Structuring Training

Abstract

Not specified

Authors: Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath

Date Published: 29th Mar 2018

Publication Type: Journal

A brief history of COMBINE
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"

Abstract (Expand)

Standards for data exchange are critical to the development of any field. They enable researchers and practitioners to transport information reliably, to apply a variety of tools to their problems, and … to reproduce scientific results. Over the past two decades, a range of standards have been developed to facilitate the exchange and reuse of information in the domain of representation and modeling of biological systems. These standards are complementary, so the interactions between their developers increased over time. By the end of the last decade, the community of researchers decided that more interoperability is required between the standards, and that common development is needed to make better use of effort, time, and money devoted to this activity. The COmputational MOdeling in Biology NEtwork (COMBINE) was created to enable the sharing of resources, tools, and other infrastructure. This paper provides a brief history of this endeavor and the challenges that remain.

Authors: Chris J. Myers, Gary Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novere, David P. Nickerson, Falk Schreiber, Dagmar Waltemath

Date Published: 1st Dec 2017

Publication Type: InProceedings

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COVID-19 Disease Map

Abstract (Expand)

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special … issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.

Authors: F. Schreiber, G. D. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, D. Walthemath

Date Published: 12th Feb 2017

Publication Type: Not specified

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