FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.
- People (18)
- Institutions (5)
- Investigations (0+1)
- Data files (7+6)
- Models (0+1)
- SOPs (0+3)
- Publications (6)
- Presentations (22+32)
- Events (7+5)
Software Engineer and Architect working within the FAIRDOM team.
Leading the development of SEEK and RightField.
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Training material, FAIRDOM user meeting, ErasysApp Funders, Glycon proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW)
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
Projects: FAIRDOM, Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Kinetics on the move - Workshop 2016, Training material, FAIRDOM user meeting, MS-DILI
Data management and standardization expert for systems biology and systems medicine, responsible for the data management user requirements and user contacts within the German LiSyM network (Liver Systems Medicine: http://lisym.org/) and associated to the FAIRDOM team.
Involved in different standardization initiatives and committees, i.e. COMBINE (http://co.mbine.org), ISO/TC 276 Biotechnology (https://www.iso.org/committee/4514241.html), European COST action CHARME (http://www.cost-charme.eu) and
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Training material, SBEpo - Systems Biology of Erythropoietin
I am group leader of the SDBV (Scientific Databases and Visualisation) group at the HITS gGmbH, the Heidelberg Institute for Theoretical Studies.
I am interested in finding data. Starting with my master's thesis I have always worked on how to store data in a way that you can find it, and how to make sense out of data that has been stored.
Within FAIRDOM I find interesting to help people to store their data in a way that they make sense even after years.
Projects: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Report of the Data Management Foundry Workshop,
19th-20th of March, 2012, Vienna, Austria
Contributor: Natalie Stanford
The tutorial provided for EraSysAPP PALs. Covers new features associated with generating snapshots, research objects, and assigning DOIs to investigation snapshots in order to make them citable structures.
Creator: Natalie Stanford
Contributor: Natalie Stanford
Date Published: 2012
Journal: Knowledge Engineering and Knowledge Management
Citation: Lecture Notes in Computer Science 7603 : 438
Author: Smallbone K.,Messiha H. L.,Carroll K. M.,Winder C. L.,Malys N.,Dunn W. B.,Murabito E.,Swainston N.,Dada J. O.,Khan F.,Pir P.,Simeonidis E.,Spasic I.,Wishart J.,Weichart D.,Hayes N. W.,Jameson D.,Broomhead D. S.,Oliver S. G.,Gaskell S. J.,McCarthy J. E.,Paton N. W.,Westerhoff H. V.,Kell D. B.,Mendes P.
Date Published: 9th Jul 2013
Journal: FEBS Lett
PubMed ID: 23831062
Citation: FEBS Lett. 2013 Sep 2;587(17):2832-41. doi: 10.1016/j.febslet.2013.06.043. Epub 2013 Jul 4.
Date Published: 7th Apr 2016
Journal: Interface Focus
PubMed ID: 27051515
Citation: Interface Focus. 2016 Apr 6;6(2):20150103. doi: 10.1098/rsfs.2015.0103.
Authors: Katy Wolstencroft, Olga Krebs, Jacky Snoep, Natalie Stanford, Finn Bacall, Martin Golebiewski, Rostyslav Kuzyakiv, Quyen Nguyen, Stuart Owen, Jakub Straszewski, Alan Williams, Bernd Rinn, Wolfgang Müller, Carole Goble, Soiland-Reyes S.,van Niekerk D. D.,Malmstrom L.
Date Published: 3rd Dec 2016
Journal: Nucleic Acids Res
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2016 Nov 28. pii: gkw1032.
Authors: Carole Goble, Katy Wolstencroft, Wilkinson M. D.,Dumontier M.,Aalbersberg I. J.,Appleton G.,Axton M.,Baak A.,Blomberg N.,Boiten J. W.,da Silva Santos L. B.,Bourne P. E.,Bouwman J.,Brookes A. J.,Clark T.,Crosas M.,Dillo I.,Dumon O.,Edmunds S.,Evelo C. T.,Finkers R.,Gonzalez-Beltran A.,Gray A. J.,Groth P.,Grethe J. S.,Heringa J.,'t Hoen P. A.,Hooft R.,Kuhn T.,Kok R.,Kok J.,Lusher S. J.,Martone M. E.,Mons A.,Packer A. L.,Persson B.,Rocca-Serra P.,Roos M.,van Schaik R.,Sansone S. A.,Schultes E.,Sengstag T.,Slater T.,Strawn G.,Swertz M. A.,Thompson M.,van der Lei J.,van Mulligen E.,Velterop J.,Waagmeester A.,Wittenburg P.,Zhao J.,Mons B.
Date Published: 16th Mar 2016
Journal: Sci Data
PubMed ID: 26978244
Citation: Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18.
Authors: Carole Goble, Olga Krebs, Waltemath Dagmar,Bergmann Frank T.,Chaouiya Claudine,Czauderna Tobias,Gleeson Padraig,Golebiewski Martin,Hucka Michael,Juty Nick,Le Novère Nicolas,Mi Huaiyu,Moraru Ion I.,Myers Chris J.,Nickerson David,Olivier Brett G.,Rodriguez Nicolas,Schreiber Falk,Smith Lucian,Zhang Fengkai,Bonnet Eric
Date Published: 15th Mar 2014
Journal: Stand. Genomic Sci.
This document helps Horizon 2020 beneficiaries make their research data findable, accessible, interoperable and reusable (FAIR), to ensure it is soundly managed. Good research data management is not a goal in itself, but rather the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse. Note that these guidelines do not apply to their full extent to actions funded by the ERC. For information and guidance concerning Open Access and the
Creator: Olga Krebs
Contributor: Olga Krebs
The presentation was given during the PALs meeting in Munich on Dec. 10th, 2015
It talks about openBIS, an open, distributed system for managing biological information.
The main goal of openBIS is to support biological research data workflows from the source (i.e. the measurement instruments) to data processing and analyzing facilities.
Creator: Rostyslav Kuzyakiv
Contributor: Rostyslav Kuzyakiv
Written and presented by Carole Goble (University of Manchester) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.
Contributor: Natalie Stanford
This event is a jointly organized Data Management PALs Meeting that involves PALs from the German LiSyM (Liver Systems Medicine) network and from the ERASysAPP (ERA-Net for Systems Biology Applications) initiative. PALs (Project Area Liaisons) are the front line experts of the data management teams of these projects. They act as data management advocates and help gathering user requirements and testing potential data management solutions. An important part of the meeting will be to gather the
Start Date: 2nd May 2017
End Date: 3rd May 2017
Event Website: Not specified
City: 36088 Hünfeld bei Fulda
FAIRDOM team is inviting all PALs to participate in the second FAIRDOM PALs meeting. The event will take place on Dec. 9-10th , 2015 in Munich, immediately after the ERAsysAPP exchange meeting scheduled for Dec 8-9th.
Beginning at 14:00 on Dec 9h, it will continue till 13:00 on Dec. 10th. Please, consider this when booking your plane/train tickets as well as hotel rooms.
The FAIRDOM team considers the meeting as an opportunity to update the PALs on available data/model management solutions, recent
Start Date: 9th Dec 2015
End Date: 10th Dec 2015
Event Website: Not specified
The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). Over the past 22 years the ISMB conference has grown to become the world's largest bioinformatics/computational biology conference. Joining forces with the European Conference on Computational Biology (14th Annual Conference) ISMB/ECCB 2015 will be the year's most important computational biology event globally.
The BBSRC has recently funded the UK Multiscale Biology network, motivated by BBSRC strategic discussions which identified ‘Multi-Scale Biology’ (MSB) as a key area of research and capability that will be at the forefront of bioscience research over the next 5-10 years. The network will aim to:
• facilitate the exploitation of areas of synergy between researchers across the UK in the broad area of multi-scale biology (MSB);
• raise awareness of the benefits of MSB;
• identify areas that are most
Start Date: 1st Jun 2015
End Date: 1st Jun 2015
Country: United Kingdom
This workshop is for computational biologists and experimentalists who wish to learn about standards, citeable data, about how to make scientific results sustainable, available through open repositories, and about how to find and reuse other people’s works. It comprises of a mixture of lectures and hands-on sessions. We will teach you the major standards and tools that support these standards, as well as steps towards encoding and publishing reproducible modeling results. Topics include data
Start Date: 14th Sep 2015
End Date: 15th Sep 2015
1st FAIRDOM + EraSysApp PALs meeting will be co-located with ERASysAPP – EXCHANGE: Networking and Info Day in Berlin, on 16 -17 April 2015
ABION Spreebogen Hotel, Salon Charlottenburg
18:00 -22:00 Social gathering and informal presentations with FAIRDOM team + old PALs +new PALs (with food and drinks served)
ABION Spreebogen Hotel, Salon Bellevue
9:00 -9:15 Short introduction from funders (Christian Rückert, PtJ)
9:15 -10.00 Warming up FAIRDOM, FAIRDOMHub and openSEEK
Start Date: 16th Apr 2015
End Date: 17th Apr 2015
Event Website: Not specified
Semantic web applications and tools for life science.
Since 2008, the SWAT4LS Workshop has provided a platform for the presentation and discussion of the benefits and limits of applying web-based information systems and semantic technologies in the domains of health care and life sciences.
SWAT4LS will provide the same open and stimulating environment that has previously brought together researchers, developers, and users, from various fields including eHealth, biomedical and clinical informatics,