Olga Krebs

About Olga Krebs:

I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In SySMO-DB project (http://www.sysmo-db.org) I was responsible for metadata design (SEEK), conceptual and logical modelling of experimental data (JERM), now our team continue this work as FAIRDOM project (http://fair-dom.org/).

SEEK ID: https://seek.lisym.org/people/8

Location:  Germany

Expertise: big data, Systems Biology, Genetics, wet lab

Tools: SEEK, openBis, Protege, Copasi, JWS online RightFiled

ORCID: Not specified

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LiSyM-Krebs

LiSyM-Krebs ist ein nationales Forschungsnetz zur Früherkennung und Prävention von Leberkrebs, das unter Verwendung des systemmedizinischen Forschungsansatzes die komplexen, dynamischen Prozesse der Krankheitsprogression analysiert, um ausgehend von den Erkenntnissen aus dem Forschungsnetz LiSyM die Entstehung von Leberkrebs besser zu verstehen, vorherzusagen und im besten Fall sogar zu verhindern.

Projects: LiSyM-Krebs Partnering, LiSyM-Krebs

Web page: Not specified

LiSyM: Liver Systems Medicine

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Web page: https://www.lisym.org/

The Hedgehog Signalling Pathway (LiSyM-JGMMS)

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Programme: LiSyM: Liver Systems Medicine

Public web page: http://www.lisym.org/our-work/junior-group/hedgehog-influences

Start date: 1st Jan 2016

LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP)

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LiSyM-Krebs

LiSyM-Krebs

Programme: LiSyM-Krebs

Public web page: Not specified

LiSyM network

This comprises the whole LiSyM network

Programme: LiSyM: Liver Systems Medicine

Public web page: http://www.lisym.org

Start date: 1st Jan 2016

LiSyM-Krebs Partnering

This generic project is intended to be a forum for all LiSyM partner and external stakeholders interested in participating in the BMBF initiative LiSyM-Krebs.

Programme: LiSyM-Krebs

Public web page: https://www.ptj.de/projektfoerderung/gesundheitsforschung/lisym-krebs

HITS gGmbH

Country:  Germany

City: 69118 Heidelberg

Web page: https://www.h-its.org/

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Meeting minutes
LiSyM-Krebs

Documents submitted to BMBF

Submitter: Olga Krebs

Investigation: 1 hidden item

Assays: Meeting minutes 2021, Meeting minutes 2022

Documents submitted to BMBF
LiSyM-Krebs

Documents submitted to BMBF

Submitter: Olga Krebs

Investigation: 1 hidden item

Assays: Project deliverables 2021, Project deliverables 2022, Project proposals

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Project deliverables 2022
LiSyM-Krebs

Project deliverables 2022

Submitter: Olga Krebs

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: Documents submitted to BMBF

Project deliverables 2021
LiSyM-Krebs

Project deliverables 2021

Submitter: Olga Krebs

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: Documents submitted to BMBF

Meeting minutes 2022
LiSyM-Krebs

Meeting minutes 2022

Submitter: Olga Krebs

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: Meeting minutes

Meeting minutes 2021
LiSyM-Krebs

Meeting minutes 2021

Submitter: Olga Krebs

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

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Project proposals
LiSyM-Krebs

Project proposals

Submitter: Olga Krebs

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: Documents submitted to BMBF

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Sample Collection and Preservation of Blood and Endometrial Tissue
LiSyM PALs

This SOP - Standard Operating Procedure for Sample Collection and Preservation of Blood and Endometrial Tissue were developed at NIH University of California San Francisco Human Endometrial Tissue and DNA Bank by Elizabeth Sheldonand, Ramsey A McIntire

Creators: Olga Krebs, Martin Golebiewski, Elizabeth Sheldonand, Ramsey A McIntire

Submitter: Olga Krebs

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The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

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

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research
LiSyM Core Infrastructure and Management (LiSyM-PD)

Abstract (Expand)

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. … It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship.

Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble

Date Published: 3rd Dec 2016

Publication Type: Not specified

Poster at SBMC 2018: Data Needs Structure: Data and Model Management for Systems Biology and Systems Medicine
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Poster presentation at SBMC 2018 (Bremen)

Creators: Martin Golebiewski, Olga Krebs, Hadas Leonov, Wolfgang Müller, Stuart Owen, Maja Rey, Natalie Stanford, Andreas Weidemann, Ulrike Wittig, Katy Wolstencroft, Jacky L. Snoep, Carole Goble

Submitter: Martin Golebiewski

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