Projects: Working Group Nicole Radde
Institutions: University of Stuttgart
https://orcid.org/0000-0002-5300-0915
Projects: BioCreative VII
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Projects: FAIRDOM, BioCreative VII
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
I am a biochemist & bio-informatician working in phytobacteriology at the Plant Sciences Unit of ILVO, the Flanders Research Institute for Agricultural, Fisheries and Food Research. The focus is on genomics-based research and diagnostics for Plant Health.
My expertise is 'wet-lab' work (microbiology, sequencing, molecular biology, design & validation of diagnostics assays using qPCR/LAMP, automatisation) and 'dry-lab' work such as bio-informatics/data analysis (e.g. scripting analysis ...
Projects: COVID-19 Disease Map
Institutions: National Institute of Informatics
https://orcid.org/0000-0001-8725-3366
Projects: Kinetics on the move - Workshop 2016, COVID-19 Disease Map, NMTrypI - New Medicines for Trypanosomatidic Infections, CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation
Institutions: Kinetics on the move Workshop at HITS, Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Eastern Finland (UEF)
https://orcid.org/0000-0002-2801-8902
Projects: MPIEvolBio-SciComp
Institutions: Max Planck Institute for Evolutionary Biology
https://orcid.org/0000-0002-2579-5546
I'm heading the Scientific Computing Unit at Max Planck Institute for Evolutionary Biology in Plön, Germany. My interest is the application of high performance and high throughput computing in data processing, data analysis, and numerical simulations of dynamical processes. I have a background in Theoretical Physics with a Ph.D. from Rostock University (2008), where I studied analytical models and numerical simulations of extremely dense and hot matter.
After a postdoc at the Lawrence Livermore ...
Projects: COVID-19 Disease Map
Institutions: University of Tübingen
https://orcid.org/0000-0002-0248-6679
Projects: COVID-19 Disease Map
Institutions: University Maastricht
https://orcid.org/0000-0002-7770-620X
Projects: Working Group Nicole Radde
Institutions: University of Stuttgart
https://orcid.org/0000-0003-3954-8981
My research interest is in studying cellular and molecular pathways of COVID-19 disease.
Projects: COVID-19 Disease Map
Institutions: Monash University
https://orcid.org/0000-0002-9207-0385
Projects: COVID-19 Disease Map
Institutions: Pondicherry University
https://orcid.org/0000-0003-4854-8238
PhD Student at Centre for Bioinformatics, Pondicherry University, Pondicherry, India.
Projects: Not specified
Institutions: Not specified
Projects: COVID-19 Disease Map
Institutions: Ontario Institute for Cancer Research
https://orcid.org/0000-0002-4650-631X
Projects: COVID-19 Disease Map
Institutions: European Molecular Biology Laboratory
https://orcid.org/0000-0002-7249-9379
Projects: CoolWine
Institutions: Norwegian University of Science and Technology
PhD candidate working on the CoolWine project
Projects: COVID-19 Disease Map
Institutions: University of Tübingen
https://orcid.org/0000-0003-3851-9978
Projects: COVID-19 Disease Map
Institutions: University of Tübingen
https://orcid.org/0000-0002-1240-5553
Andreas Dräger is the assistant professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens at the University of Tübingen in Germany. His group aims to combat the spreading antibiotics resistances by using mathematical modeling and computer simulation of bacterial systems up to entire microbiomes and host-pathogen interactions. In doing so, his group actively contributes to the advancement of various COMBINE standards.
Projects: COVID-19 Disease Map
Institutions: Monash University
https://orcid.org/0000-0002-1788-9593
Projects: COVID-19 Disease Map
Institutions: University of Pittsburgh
Projects: COVID-19 Disease Map
Institutions: Barcelona Supercomputing Center
https://orcid.org/0000-0002-7696-1241
I completed my BSc in Biology and MSc in Cell Biology by the University of Valencia. During my last undergrad year I participated in synthetic biology’s iGEM competition where I dove in the use of models in Biology, which pushed me to pursue a PhD in the Department of Applied Mathematics in the Technical University of Valencia.
My research on Metabolic Engineering of hydrogen in cyanobacteria led me to be visiting researcher at Uppsala University, Denmark Technical University and EMBL Heidelberg. ...
Projects: COVID-19 Disease Map
Institutions: ICAHN Icahn School of Medicine at Mount Sinai
https://orcid.org/0000-0002-1605-8130
Experienced in developing rule-based models of complex biochemical reaction networks, as well as developing new rule-based approaches. Extensive experience with BioNetGen, a tool for building complex reaction networks succinctly with rules. Currently working with Jonathan Karr at Dept. Genetics & Genomics at Mount Sinai School of Medicine on extending rule-based approaches to transcription, translation and other sequence-based mechanisms.
Polyglot European Scientist. I thrive working in interdisciplinary environments combining the study of enzyme reactions and mechanisms with bioinformatics, molecular modelling, automated data analysis and data stewardship.
Projects: pISA-tree, HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, tst, tst2
Institutions: National Institute of Biology, tst
https://orcid.org/0000-0002-1669-6482
Computational Biologist and Biostatistician at Department of Biotechnology and Systems Biology, National Institute of Biology (NIB)
Projects: WG Infrastructure for Translational Research, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Translational Bioinformatics, Medical Biometry, Epidemiology, Medical Informatics
Institutions: University Medical Center Göttingen, University of Tübingen, University of Saarland
https://orcid.org/0000-0002-1505-594X
Institutions: Latvia University of Agriculture
Lutz Brusch is heading the research group "Spatio-temporal pattern formation in cells and tissues" at the Centre for Information Services and High Performance Computing of TU Dresden, Germany. The group is co-developing the multi-cellular modelling and simulation framework Morpheus (https://morpheus.gitlab.io) and is collaborating with experimental labs on questions of tissue morphogenesis and regeneration.
Projects: OXYMOD
Institutions: Norwegian University of Science and Technology
https://orcid.org/0000-0002-1644-3223
Projects: COMBINE Multicellular Modelling
Institutions: Indiana University Bloomington
https://orcid.org/0000-0002-7440-2905
Research Associate in the Macklin Lab, School of Informatics, Computing, and Engineering. Indiana University, Bloomington, IN USA.
Projects: COMBINE Multicellular Modelling
Institutions: University College London (UCL)
https://orcid.org/0000-0001-5963-8576
Projects: SAFE-Aqua, Biomics Projects
Institutions: Institut Pasteur
https://orcid.org/0000-0001-6286-1138
Projects: DigiSal, GenoSysFat, SAFE-Aqua, Unlock
Institutions: Wageningen University & Research
https://orcid.org/0000-0001-8172-8981
Biochemist currently keeping busy as: Research Data Manager (Vrije Universiteit Amsterdam), Software Engineer (Heidelberg University) and member of the SBML Development Team (Caltech).
Projects: EmPowerPutida
Institutions: LifeGlimmer GmbH
Computational Biologist
I am a researcher (PhD student) working at Wageningen University & Research as bioinformatician and modeller. I am working as part of the MycoSynVac (http://www.mycosynvac.eu/) project on dynamic modelling of central carbon metabolism in M. pneumoniae, to be extended to full dynamic modelling of metabolism to be implemented in a whole cell model. I am also looking into possibilities to improve standards in model generation using semantic technologies, improving automatic generation, annotation ...
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, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COMBINE Multicellular Modelling, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, NMTrypI - New Medicines for Trypanosomatidic Infections, ModeleXchange initiative, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, BioCreative VII
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-4980-3512
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: Kinetics on the move - Workshop 2016
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Research associate at HITS, software developer
Projects: FAIRDOM
Institutions: ETH Zurich & Basel / The Scientific IT Services (SIS) division
Head of Scientific IT Services and member of the ITS executive board at ETH Zurich. Project manager of SyBIT. Project partner of the FAIRDOM Initiative.
I hold a Medical Doctor Diploma (Lviv, Ukraine) with the specialization in General Medicine. After the graduation from the Post Graduate Program in Bioinformatics at the Seneca College/York University (Toronto, Canada), I successfully participated in the number of scientific projects conducted at the University of Toronto (Canada) and the Toronto East General Hospital (Canada).
I obtained the PhD in Bioinformatics at the Swiss Institute of Bioinformatics (Geneva, Switzerland). As a PhD student, ...
Projects: SysMetEx, Kinetics on the move - Workshop 2016
Institutions: Università della Svizzera Italiana
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, FAIRDOM Templates
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-4958-0184
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Projects: TRANSLUCENT
Institutions: Humboldt-Universität zu Berlin
I created this for all SysMo Modellers
http://www.semanticsbml.org/aym Annotate Your Model
There you can annotate your non SBML models with biological terms (MIRIAM annotations). As a cool extra you can view you model source code with inserted biological infomation.
Together with this http://www.semanticsbml.org/semanticSBML you can serach for similar BioModels. The similarity search is based on MIRIAM annotations that are attached to you model. AYM also allows you to create annotations without ...
Projects: KOSMOBAC
Institutions: University of Aberdeen
Physicist, working on the modelling side.
Projects: TRANSLUCENT
Institutions: Humboldt-Universität zu Berlin
Projects: BaCell-SysMO
Institutions: University of Goettingen
I'm a PhD student at the lab of Prof. Dr. Jörg Stülke. My main interest is to analyze the central metabolism of Bacillus subtilis using systems biology software. I have developed an algorithm to find short pathways connecting sets of metabolites and I'm also involved in SubtiWiki, the wiki for all genes of Bacillus subtilis (http://subtiwiki.uni-goettingen.de)
Projects: Noisy-Strep
Institutions: University of Cologne
I am a phd student working on statistical physics and complex systems and applying concepts from these fields to biology.
Assessment of the possible multiple correlation between experimentally determined TbPTR1 and TbDHFR inhibition values and corresponding anti-parasitic activities against T. brucei brucei bloodstream forms using a Python script.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Assessment of possible linear correlations between predicted ADMET descriptors from QikProp (Schrödinger, LLC, New York, NY) runs and experimentally determined activities against T. brucei brucei bloodstream forms with the help of a Python script.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Assay: A05BUSCO Short Name: 05BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO post filtering and reassignment Description: BUSCO post filtering and reassignment pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/pathtofiles.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: A02.7VecScreen Short Name: 02.7VecScreen Assay Class: DRY Assay Type: VecScreen Title: VecScreen on raw tr2aacds output Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/pathtofiles.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: A02.3InterProScan Short Name: 02.3InterProScan Assay Class: DRY Assay Type: InterProScan Title: InterProScan on tr2aacds output Description: InterProScan on tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/pathtofiles.txt
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: A02.1BUSCO Short Name: 02.1BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO on assemblies and tr2aacds output Description: BUSCO on assemblies and tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/pathtofiles.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
This is the analysis part of the Simulation Foundry, Version 1.5.
Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.
Make sure you followed the instructions in "Preparation" before running this.
Submitter: Gudrun Gygli
Biological problem addressed: various analyses of molecular dynamics simulations
Investigation: 1 hidden item
This is the simulation part of the Simulation Foundry, Version 1.5.
Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.
Make sure you followed the instructions in "Preparation" before running this.
Submitter: Gudrun Gygli
Assay type: Molecular Dynamics
Technology type: All-Atom
Investigation: 1 hidden item
Preparation needed to use Simulation Foundry, Version 1.5.
Please read the manual before working with this Simulation Foundry.
Pay careful attention to the installation instructions.
Note the known issues.
Submitter: Gudrun Gygli
Assay type: Instructions
Technology type: Technical Computer Installation
Investigation: 1 hidden item
This is a collection of data that have been used to analyse data on deep eutectic solvent mixtures of choline chloride:glycerol:water.
Submitter: Gudrun Gygli
Biological problem addressed: Model Analysis Type
Investigation: Deep Eutectic Solvents
Zip-file with Python module used to calculate trivariate statistics between the inhibition of parasitic target enzymes pteridine reductase 1 and dihydrofolate reductase and the corresponding inhibition of T. brucei brucei bloodstream forms. The script makes use of an expansion of pairwise Pearson or Spearman correlations. For further details, also refer to the README file.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
DownloadZip file with Python module used to correlate compound descriptors predicted with Schroedinger QikProp with observed anti-parasitic effect against T. brucei brucei bloodstream forms. The script allows a leave-one-out analysis in addition to the default correlation analysis, where data for each compound is skipped once before the correlation analysis is re-performed. An example config file is provided with the zip-archive. For further instructions and information on the available settings, also ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Python script wrapping up (executing) all the steps of the workflow the user enters in it. Together with "names.py" this script requires input files to be located in a folder called "input" in the same directory.
Creators: Gudrun Gygli, Juergen Pleiss, Xinmeng Xu
Submitter: Gudrun Gygli
Python script allowing the user to define the names of the input files to be used. Together with "wrapper.py" this script requires input files to be located in a folder called "input" in the same directory.
Creators: Gudrun Gygli, Juergen Pleiss, Xinmeng Xu
Submitter: Gudrun Gygli
Python workflow for the analysis of ITC-BIND, ITC-MIM and ITC-(r)SIM experiments. Organized in a *.zip folder. Requires the following directory structure:
./ITCanalysis.py ./input/BINDING/.apj ./input/BINDING/.csv ./input/KINETICS/.apj ./input/KINETICS/.csv ./scripts/bindingneu.py ./scripts/kinetics_neu.py
And can be executed by running python ITCanalysis.py in the directory. Filenames for the input *.apj and *.csv files are defined in ITCanalysis.py. The output directory is written by ...
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Instructions and details on the data analysis workflow.
Creators: Gudrun Gygli, Juergen Pleiss, Xinmeng Xu
Submitter: Gudrun Gygli
Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden
Date Published: No date defined
Publication Type: Not specified
Scripts and Input Files for Analysis V1.5
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Scripts and Input Files for Simulation V1.5
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
