Olga Krebs

Ionizing radiation (IR) leads to DNA double-strand breaks and can therefore be used as cancer treatment. However, some tumors are less responsive to radiation treatment because of their underlying molecular profile. Our ultimate goal is to understand the reaction of lung cancer cells with different phenotypes to IR on a molecular level to then provide the best therapy options for lung cancer patients with IR therapy.

OLCIR is funded by the Federal Ministry for Education and Research (BMBF, ...

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.

Collection of training material for SEEK/FAIRDOMHub

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 our users meeting you can:

• Learn why data and model management is ...

SDBV group using Hub

Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis. Theyhad and have tremendous influence on the biogeochemical cycles on Earth. Recently,cyanobacteria are increasingly investigated as cell factories for a sustainableeconomy. Despite their global, environmental and rising economic importance, ourknowledge on the regulation of their primary metabolism is fragmented.Cyanobacteria switch between photoautotrophic and heterotrophic modes ofmetabolism during day/night cycles or ...

MESI-Review 2024

MESI-STRAT: Systems Medicine of Metabolic-Signaling Networks -A New Concept for Breast Cancer Patient Stratification. Breast cancer is a complex disease with high prevalence in the European Union and world-wide. 75%-80 of the patients have estrogen receptor-positive (ER)-positive tumors and are treated with endocrine therapies. Endocrine therapies, which block ER-driven tumor growth, show high efficacy. Yet, a significant proportion of the patients will eventually relapse with metastatic breast ...

MESI-STRAT Review

PoLiMeR is funded through the EU Marie Skłodowska-Curie Innovative Training Network (ITN), which drives scientific excellence and innovation. ITNs bring together universities, research institutes, industry and clinical partners from across the world to train researchers to doctorate level.

Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease ...

Microalgae Microbiomes: A natural source for the prevention and treatment of diseases in aquaculture

Aquaculture is one of the fastest growing food sectors in the world. In order to guarantee continuous, efficient and sustainable production and to safeguard the growth of this important sector, its protection from biological threats is crucial. Within the AquaHealth project, an international consortium of highly experienced partners will assemble and apply an advanced meta’omics toolbox on the ...

The project "INtegrative COllaborative modeling in systems MEdicine" aims at connecting different heterogenous datasets and individual models within systems medicine.

Using standard systems biology methodologies a 14-compartment dynamic model was developed for the Corona virus epidemic. The model predicts that: (i) it will be impossible to limit lockdown intensity such that sufficient herd immunity develops for this epidemic to die down, (ii) the death toll from the SARS-CoV-2 virus decreases very strongly with increasing intensity of the lockdown, but (iii) the duration of the epidemic increases at first with that intensity and then decreases again, such that ...

Amino alcohol moieties are found in highly diverse classes of natural products that are of great importance due to their bioactivity, and they function as chiral building blocks for the synthesis of pharmaceuticals and agrochemicals. The chemical synthesis of stereoisomerically pure amino alcohols is difficult and typically requires uneconomical steps for protective group manipulations. Conventional syntheses in the chemical industry often use hazardous substances, consume large amounts of energy ...

to complete

The GMDS project group bundles activities for health-related FAIR data infrastructures in the fields of biomedical research, clinical data management and medical informatics in Germany. It aims at providing a platform for information exchange about best practice for and implementation of FAIR data management in these fields and constructing a network of FAIR data managements providers in these fields. Through bridging between providers and potential users of such data management platforms within ...

Here we collect curated data to be integrated into public repositories

Current chemical concept recognition tools have demonstrated significantly lower performance for in full-text articles than in abstracts. Improving automated full-text chemical concept recognition can substantially accelerate manual indexing and curation and advance downstream NLP tasks such as relevant article retrieval. Participating in BioCreative Track NLM-Chem we focus identifying chemicals in full-text articles (i.e. named entity recognition and normalization).

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 ...

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 ...

Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped ...

Sequence data for European Nucleotide Archive (ENA ) https://www.ebi.ac.uk/ena/

Metabolomics data a for Metabolight DB

Proteomics data for PRIDE, UniProt and others

Chemical named entity recognition (NER) is a significant pre-processing task in natural language processing. Identification and extraction of chemical entities from biomedical literature and entities linking to the knowledge base are essential steps for the chemical text-mining pipeline. However, the identification of chemical entities in a biomedical text is a challenging task due to the diverse morphology of chemical entities and the different types of chemical nomenclature. In this work, we ...

Experimental study for hands on session

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

we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue completely dependent on sucrose supply from the mesophyll ...

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)

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

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.

Here we will use JERM templates with embedded ontologies to describe and annotate example data

Here we will use JERM templates with embedded ontologies to describe and annotate example data 222

Usage of fine-tuned BioBERT for identification of chemical entities

Using semantic search in MesH and PubChem databases for entity linking

Here we present ENA-requirements compliant template and SOP for submission steps

Excel template for metadata required by ENA to submit sequence data

An example template for MAGE-TAB compliant transcriptomics data. This example only covers the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF) worksheets (i.e. the metadata from a microarray experiment). This template was generated automatically using the ArrayExpress submission help tool (http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi)

Global microRNA expression profiling of high-risk ER+ breast cancers from patients receiving adjuvant Tamoxifen mono-therapy: a DBCG study

GEO Data set GSE9893 : A gene expression signature predicting the recurrence of tamoxifen-treated primary breast cancer.

Shared version of Publication "Welcome to the Family: Identification of the NAD+ Transporter of Animal Mitochondria as Member of the Solute Carrier Family SLC25"

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

Master template for hands on session

Excel sheet template : concentrations of intracellular metabolites

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.

Here published artikel about The FAIR Guiding Principles for scientific data management and stewardship

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

test file

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

MIAPE based Gel Electrophoresis Data Entry Worksheet

Final version of the Agenda: All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock.

Please fill in thistravel expense reimbursement report and send it together with original receipts to HITS

Meeting location map

How to get to the hotel from rail station

The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that ...

Standard Operating Procedure (SOP) for integration of MESI-STRAT sequence data stored in MESI-SEEK into ENA

A Standard Operating Procedure (SOP) is a document consisting of step-by-step information on how to execute a task. An existing SOP may need to just be modified and updated.

Standard Operating Procedure for human genomic DNA extraction ( copied from GEO DataSets GSM1375121)

Standard Operating Procedure describes the labeling of eukaryotic RNA with aminoallyl labeled nucleotides via first strand cDNA synthesis followed by a coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules (published by The Institute For Genomic Research

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

The procedure describes the preparation of fluorescent DNA probes from human mRNA or total RNA.

Written Standard Operating Procedures provide workers with the operational information necessary to perform a job properly and ensure consistency in the operations. Standard Operating Procedures provide a historical record of steps in the how, why and when and serve as a training tool for teaching users.

FAIRDOM: hands-on basic training

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

COVID-19 modelling efforts in advice to Luxembourg government , talk given by Atte Aalto

Hands on session given by Olga Krebs

FAIRDOMHub: Implementing FAIR Data Principles for scientific data management and stewardship. Talk given by Olga Krebs

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 ...

Step-by-step instructions for hands on session

Talk by Jon Olav Vik, Norwegian University of Life Sciences

Talk given by Tomasz Zieliński

Talk given by Sergey Lashin from Institute of Cytology and Genetics, Novosibirsk, Russia

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

Talk by Jacky Snoep, Stellenbosch University, SA

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

Agenda:

14:00 - Welcome

14:10 - Korbinian Bösl (University of Bergen, Norway): “Integrating FAIRDOM-SEEK with storage and data management planning tools”

14:30 - Martin Golebiewski, Xiaoming Hu (HITS, Germany), **Frank Meineke **(University of Leipzig, Germany): “Extended metadata feature of SEEK in the Local Data Hub of NFDI4Health”

14:50 - Nick Juty (University of Manchester, UK): “SOPs in WorkflowHub”

15:10 - Charles Demurjian (Massachusetts Institute of Technology, US): ...

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

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 ...

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, ...

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

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 ...

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, ...

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 ...

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 ...

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 ...

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 ...

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)