FAIRDOM

FAIRDOM is establishing a support and service network for European Systems Biology. FAIRDOM is a joint action of ERA-Net ERASysAPP and European Research Infrastructure ISBE to establish a data and model management service facility for Systems Biology. Our prime mission is to support researchers, students, trainers, funders and publishers by enabling Systems Biology projects to make their Data, Operating procedures and Models, Findable, Accessible, Interoperable and Reusable (FAIR).

Data integration is an essential part of Systems Biology. Scientists need to combine different sources of information in order to model biological systems, and relate those models to available experimental data for validation. Currently, only a small fraction of the data and models produced during Systems Biology investigations are deposited for reuse by the community, and only a smaller fraction of that data is standards compliant, semantic content. By embedding semantic technologies into familiar ...

Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex cellular pathways and ...

Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources

Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.

These templates can be used for a selection of metabolomics data types. There is a MASTER template for general use and adaptation as well as several more specific templates for particular types of experiment (e.g. HPLC), or specific assay types (e.g glucose pulse)

This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.

Dear SEEK users, this Assay is just an example Excel sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat

Some examples of transcriptomics templates for Affymetrix data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

A example of an RT-PCR Excel template. RT-PCR is Reverse Transcriptase PCR (NOT to be confused with Real Time PCR, which is normally referred to as qPCR)

This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using templates will mean easier submission to public databases on publication and greater consistency of data in SEEK.

This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model). Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.

Some examples of transcriptomics templates for NimbleGen data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using templates will mean easier submission to GEO/ArrayExpress upon publication and greater consistency of data in SEEK for easier searching and comparing.

Examples of proteomics templates for gele electrophoresis data that conform to the MIAPE-GE specification

Some generic examples of transcriptomics templates that conform to the MAGE-TAB specification. These templates were created and modified from templates produced by ArrayExpress and GEO. These templates are generic and non-specific for any particular array platform.

Some examples of proteomics templates for Mass Spectrometry data that conform to the MIAPE specification

Deatiled agenda forBest practices in research data management and stewardship (2021-06-14)

Excel sheet template : concentrations of intracellular metabolites

Report of the Data Management Foundry Workshop, 19th-20th of March, 2012, Vienna, Austria

Tutorial given at the Reproducible and Citable Data and Models Workshop, Warnemunde September 14th-16th 2015.

a test file

Agenda for the satellite data management tutorial of Synthetic Biology 2017.

3rd ERASysAPP – EXCHANGE Day: Networking and Info Day for research projects of the first and second ERASysAPP calls

List of participants/1st EraSysApp PALs meeting

Participants of 2nd FAIRDOM PALs meeting in Munich

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.

This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model). Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.

This is not my model

This guidlines has been developed by Rita Volkers from Wageningen University for IBISBA project, as example to use

Talk given by Olga Krebs and Aleyey Kolodkin at the" Best practices in research data management and stewardship" training on 17 June 2021

FAIRDOM introduction by Olga Krebs

Introductory talk given by Olga Krebs in the Department of Chemical Engineering at the University of Rovira i Virgili on 19th of July 2017

Introductory talk given by Olga Krebs in the Department of Chemical Engineering at the University of Rovira i Virgili on 19th of July 2017

SEEK functionalities presented by Olga Krebs

Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016

FAIRDOMHub training for SYSTERACT project meeting on 10th of November 2016 in Leiden, NL

Talk given by Olga Krebs at FAIRDOM-LiSyM-de.NBI Data Structuring Course - Nov 22-23 in Hünfeld (D)

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 ...

Talk given by Tomasz Zieliński

Presented by Martin Böhm, German Cancer Research Center, Heidelberg, Germany

Talk by Jacky Snoep, Stellenbosch University, SA

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.

Slides that were presented alongside a SEEK demonstration at the EraSysApp PALS meeting in Munich - December 2015

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.

Documentation for using FAIRDOMHUB / SEEK for a workshop in Warnemunde, September 2015.

Written and presented by Carole Goble (University of Manchester) at Multiscale Biology Network Springboard meeting, Nottingham. June 1st 2015.

Written and presented by Carole Goble (University of Manchester) at Multiscale Biology Network Springboard meeting, Nottingham. June 1st 2015.

Written and presented by Wolfgang Müller (HITS) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Day 4 of Best practices in research data management and stewardship 17 June 2021. Introduction to and Hands-on training on FAIRDOMHub to manage your research assets

Managing your data and metadata well is an important research skill. Good data management enables the preparation, handling, storing, sharing, and reuse of data. These attributes of good data management equates to efficient research and saving of time and resources. Data management tools, utilizing data standards and best practices can help to make your research data and models FAIR (Findable, Accessible, Interoperable and Reusable).

SEEK, is a web-based (or locally installed) resource platform ...

FAIRDOM PALS and users meeting 2019 is happening in Heidelberg, as a satellite meeting of the COMBINE (COmputational Modeling in BIology Network) meeting. FAIRDOM is a research infrastructure offering data management support. The SEEK software is designed as registry and storage place for data, models, biological samples, processes, publications and presentations, and at the same time as yellow pages for projects, people and events. SEEK is implemented as central data management platform FAIRDOMhub ...

FAIRDOM training for HOTSOLUTE /EraCoBioTech

During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is ...

The 10th Young Scientists School “Systems biology and Bioinformatics” SBB-2018 will be held on 27–31th of August 2018 in Novosibirsk, Russia Bioinformatics is a rapidly developing field of knowledge. Each of the past Young Scientists Schools concerned topics urgent at those times. To preserve this tradition, the SBB-2016 will be dedicated to bioinformatics and systems biology in such areas as: Genomics and evolutionary bioinformatics Structural biology and molecular dynamics Molecular-genetic ...

The overarching integrating power of computational modelling, from systems biology to systems medicine

Participants will learn how to structure and share complex data in a Findable, Accessible, Interoperable and Reusable (FAIR) manner. Hands-on sessions, lectures and software demonstrations will provide attendees with the necessary skills to apply components of the FAIRDOM infrastructure in their daily work for interrelating and exchanging data, models and corresponding information.

FAIRDOM is a research infrastructure offering data management support. The SEEK software is designed as registry and ...

We are excited to announce our 2017 SynBio Data Management Training Day. The event is co-located with Synthetic Biology UK, in Manchester. The venue will be the Manchester Institute for Biotechnology (http://www.mib.ac.uk/contact/).

Topics that will be covered include - Model management in FAIRDOMHub - Publishing using FAIRDOMHub - Samples in FAIRODMHub

On top of this we will have talks about general data management using FAIRDOM, and also smart publications.

Participation is free. We have limited ...

Target audience: Wet-lab scientists and people dealing with experimental and/or clinical data for research

Topics include: - Best practice data structuring (spreadsheets) for experimental and (clinical) samples data - Comprehensive and unambiguous data description and annotation - Standard formats and terminologies for data and metadata - Guidelines for reporting data (Minimum information standards) - Annotation tools (e.g. RightField: http://www.rightfield.org.uk) - Using SEEK & FAIRDOMhub ...

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 ...

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 ...

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 ...

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 conferences ...

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 ...

1st FAIRDOM + EraSysApp PALs meeting will be co-located with ERASysAPP – EXCHANGE: Networking and Info Day in Berlin, on 16 -17 April 2015

April 16th 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)

April 17th 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 ...

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, ...

Best practices in research data management and stewardship training on 17 June 2021

Day 4. FAIRDOMHub and Zenodo Hands On Instructions (by Olga Krebs and Aleksey Kolodkin)

This is the fifth and final draft of the Recommendations and Guidelines from the RDA COVID-19 working group, and is open for public comment until 8th of June 2020. Following the open period, feedback will be considered and then the WG will seek endorsement of the document from the RDA governance bodies prior to final publication.