Events

Agenda:

14:00 - Welcome & Agenda

14:05 - Update about Samples related features in FAIRDOM-SEEK

Flora D’Anna, VIB

14:30 - Overview of the latest FAIRDOM-SEEK release

Stuart Owen, University of Manchester

14:40 - Presentation of the new roadmap

Stuart Owen, University of Manchester

15:00 - Discussion about the roadmap

15:15 - Q&A: ask me anything

The workshop “Novel leads and drugs and their mechanism of action in the field of vector borne parasitic disease” is jointly organized by WG1 “Compound libraries coordination and integration of compound design” and WG2 “Integration of early phase studies and low environmental impact actions” of the COST Action CA21111 OneHealthDrugs. The focus of the workshop is to bring together experts to report and discuss common definitions of novel leads and drugs and their mechanisms of action in view also ...

Agenda:

• 14:00 - Welcome
• 14:10 - Ulrich Sax (University Medical Center Göttingen, Germany) "A translational use case for SEEK in current cancer research"
• 14:30 - Dagmar Waltemath (University Medicine Greifswald, Germany) "Managing computational models in biology and medicine: Experiences from running FAIRDOMHubs in the COMBINE and Medical Informatics communities"
• 14:50 - Jacky Snoep (Stellenbosch University, South Africa) _"Running reproducible modelling projects on the ...

Agenda:

• 14:00 - Welcome
• 14:10 - Marek Ostaszewski (Luxembourg Centre for Systems Biomedicine, LU): “FAIRDOMHub - a platform for the research community building the COVID-19 Disease Map”
• 14:30 - Sara El-Gebali (SciLifeLab Data Centre, SE): “Samples Metadata at the SciLifeLab”
• 14:50 - Huiming Ding (Massachusetts Institute of Technology, US): “Creating mutable samples using NExtSEEK”
• 15:10 - Rafael Andrade Buono (VIB, BE): “DataHub: focusing on sample metadata”
• 15:30 - Discussion

The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2022 will be a workshop-style event with oral presentations, breakout sessions and tutorials. The three meeting days will include talks about the COMBINE standards and associated or related standardization efforts, presentations of tools using these standards, breakout sessions for detailed discussions ...

The purpose of a new series of user meetings is to establish an active FAIRDOM user community to allow networking between various FAIRDOM-SEEK users and learn from each other’s experiences. Within the two-hours event the FAIRDOM team will give an introduction on current developments and the invited users will showcase the use of FAIRDOMHub and other FAIRDOM-SEEK instances for their research projects.

Invited speakers: Cyril Pommier, Frank Meineke, Jasper Koehorst, Andrej Blejec

Date recorded: September 14 2021

Enzymes are the catalysts of life, accelerating chemical reactions in living organisms. Enzyme reactions are widely applied in industry, for example as ingredients in laundry detergents, in the production of cheese, or to synthesize pharmaceutical drugs.

To apply enzymes in industrial processes, a detailed understanding of the molecular mechanisms is needed, requiring in depth studies on their reaction mechanisms. Such mechanistic studies can be performed with ...

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

The workshop gave an in-depth introduction to data management with SEEK and openBIS, two leading open-source data management solutions. Plenary talks including use cases by "power users" of SEEK and openBIS were complemented by hands-on sessions led by professional data management trainers.

Program Day 1 of the workshop is devoted to the data sharing and dissemination platform SEEK. Day 2 will cover the integrated data management solution openBIS, featuring an Electronic Lab Notebook, Laboratory ...

Crash course of Mathematical modelling, for any learners who want to use models to better understand and assess COVID-19 policies around the world! This course aims at anyone who seeks to understand and assess the utility of mathematical models to make a prediction which could play a key role in government policymaking, as well as a research strategy for pandemic diseases such as COVID-19. The strategies of ‘learning by example’ and ‘learning by doing’ will be here instantiated as learning how ...

Protein Engineering Congress EU

This workshop will be organized by the GMDS project group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", established in early 2019. The aim of this project group is to present the activities in various projects and at different German research locations with regard to infrastructures for FAIRes (Finadable, Accessible, Interoperable, Reusable) data management. To this end, a joint exchange of experience will take place in order to plan joint concepts (e.g. dissemination of FAIR, ...

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 ...

Aim Multicellular spatial models have become an essential tool in quantitative biology and multiple model formalisms and simulation frameworks coexist. Progress towards software interoperability and reproducibility requires a novel model description language and conversion library, complementing SBML. Building on the community‘s practical experiences with multiple formalisms and simulators, we aim at (1) defining the concept for a multicellular language while simultaneously (2) exploring automated ...

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 ...

The first Digital Salmon industry workshop raised awareness of the Digital Salmon vision and engaged major industry players in discussions on data sharing and reuse, guidelines and best practices for private-public collaboration. The workshop was a success, and a Digital Salmon working group was formed, comprising industry, academia and funding bodies. Its first task is to develop a white paper to be presented to the industry in summer of 2020.

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 16th conference on Computational Methods in Systems Biology (CMSB 2018) will take place on the 12th to 14th September 2018 in Brno, Czech Republic. Its aim is to bring together researchers from across biological, mathematical, computational, and physical sciences who are interested in the study, modelling, simulation, advanced analysis, and design of biological systems.

CMSB 2018 will be hosted at Faculty of Informatics, Masaryk University, Brno. Brno is the city where the modern genetics has ...

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 ...

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 principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The second day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOM Hub/SEEK is ...

Our 2018 DigiSal project meeting is held as a satellite meeting of Digital Life 2018 (https://digitallifenorway.org/arrangementer/digitallife-2018).

Most of DS18 will be spent on breakout sessions to work on upcoming publications. Task leaders will prepare:

• Abstracts to DLN18. (Deadline was 15 Feb.) Presenting DigiSal progress here rather than at DS18 frees up time for the paper preparation sessions.

• Identify two papers in preparation, which will be worked on at DS18: Title, first and ...

Abstracts and posters from DigiSal for Digital Life 2018.

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 ...

The meeting will provide a great opportunity for discussion between modellers, experimentalists and clinicians and to organize and harmonize our future work within the LiSyM network on the grassroot level.

All PhD students as well as all PostDocs of the LiSyM network are kindly requested to register by February 1st

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 ...

Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you! At the meeting you can

• Learn why data and model management is important, ...

Approximate dates of plant growth and harvesting by Sarah Hodge and Andrew Millar, University of Edinburgh

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Here we collect all the presentations, hands on instructions and documentation for Kinetics on the move Workshop on Data for Computational Modeling

The second project review meeting took place on May 24-25, 2016, at the University of Luxembourg, Luxembourg. This was a theory meeting between the team members to discuss research progress and plans for the project.

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, ...

The kickoff meeting of CropClock team took place in November 12, 2014 at the Max Plank Institute (MPIPZ, http://www.mpipz.mpg.de/en), Kologne, Germany. The goal for this meeting was for the members of the various teams to get acquainted with each other’s expertise and to discuss the following items: 1) Logistics about the project start, 2) Data that need to be shared, 3) Matlab code that needs to shared among the teams. The initial plan of action for data sharing was also laid out.

This mini-symposium, colocated at the ECMTB in Gothenburg, presents the state-of-the-art in computational methods for multicellular systems biology. It brings together developers and users of this software to identify common approaches and future challenges concerning multiscale integration, model specification, model exchange, scalability, workflow management as well as compliance to standards and guidelines. The session thus aims to provide an overview of the available modeling and simulation ...

Approximate dates of plant growth and harvesting by Imaizumi lab, University of Washington in Seattle

Systems Biology is one of the most prominent newly emerging interdisciplinary science areas. By connecting fields such as genomics, proteomics, cell biology, medicine, molecular biology, biochemistry and genetics, with mathematics, bioinformatics, engineering and computation, it 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 eventually of whole cells are generated, which are ...

7th All hands PALs + SEEK users meeting will be co-located with Computational Modeling in Biology Network (COMBINE) meeting taking place from 16th to 20th of September 2013 in Paris. COMBINE is an initiative to coordinate the development of the various community standards and formats, details to meeting agenda and location here: http://mbine.org/events/COMBINE_2013

We plan to arrive on Wednesday, 18th, to participate in COMBINE on Thursday and Friday morning, and to have PALs- only sessions on ...

The next All Hands PALs meeting will take place on Thursday 29th and Friday 30th November 2012 in Heidelberg. The meeting will start on Thursday morning (arriving in Heidelberg on Wednesday evening), and finishing after lunch on Friday, so that you can get to home before weekend starts.

Meeting agenda

Thursday 29th November 9:15 Arriving at HITS 9:30 – 10:00 Introduction to PALs meeting 10:00 – 10:45 Review of new SEEK features. 10:45 – 11:00 Coffee break 11:00 – 12:00 An update on SEEK BioSamples ...

SysMO-LAB2 Meeting Copenhagen 2012

We've presented SEEK at the ICSB / PLATFORM Computational Tools and Algorithms on 20th of August 2012 in Toronto, Canada

The third annual COMBINE meeting took place at The Donnelly Centre building at the University of Toronto from Wednesday August 15 through Sunday Aug. 19, 2012

The 5th annual All Hands PALs meeting will take place on 21-22 of May 2012 in Rostock/Warnemünde. The main purpose of the meeting is to update the PALs on the latest developments in SysMO-SEEK and to identify new features and priorities arrising from work in the SysMO projects .

Meeting agenda:

Monday 21st of May

Morning - What's new in SEEK 9:15 – 9:45 Arrival, Introduction and welcome to new people (Wolfgang) 9:45 – 10:45 New features in SEEK & Roles (Stuart) 10:45 – 11:15 Coffee break 11:15 ...

Annual Conference of Bacillus subtilis community.

The next SySMO SEEK users meeting will be held in Berlin on March 26-27 2012. Since our last users workshop focused on modeling issues, this one will focus on experimental data and its linking to models. Meeting info is also available at our web page details here http://www.sysmo-db.org/node/53. Detailed agenda can be downloaded here https://seek.sysmo-db.org/data_files/937

Meeting will take place at the Beuth Hochschule für Technik Berlin http://www.beuth-hochschule.de/1654/, accomodation hotel ...

Progress Meeting

BaCell consotium in Groningen.

Agenda Saturday 27th August

9:15 Pick up from Hotelo hotel 9:30 – 10:00 Arrive at HITS, coffee 10:00 – 10:15 Introduction 10:15 – 11:45 Lightning Talks by PALS and SysMO-DB team *(for details see Introduction to Lightning Talks and ISBE session at PALs meeting on 27th of August in Heidelberg associated to this event http://seek.sysmo-db.org/data_files/902 ) 11:45 – 12:15 Coffee break 12: 15 – 13:00 Review of new SEEK features (presentation available as data file associated to this event here ...

The 2011 SysMO Conference.

Agenda: http://www.sysmo.net/lw_resource/datapool/__pages/pdp_157/Agenda_SysMO_Conference_2011.pdf