Well rounded biologist/biotechnologist/biochemist/enzymologist/bioinformatician/computational biologist.
Expertise: Software Engineering, constraint-based modelling, Machine Learning
Tools: Python, cobrapy toolbox
Projects: pISA-tree, HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, INDIE - Biotechnological production of sustainable indole, _p_stRT
Institutions: National Institute of Biology

Roles: PhD Student
Expertise: Data analysisMathematical modellingBioinformaticsSystems biology, Data integration, Data Management, Visualization, Data analysis, computational biology, Bioinformatics, Molecular Biology, Mathematical and statistical modeling, Statistics, Programming
Tools: Bioinformatics, Data integration, Dynamic modelling, R, Computational and theoretical biology, Data Management, Molecular Biology, Systems Biology, Computational Systems Biology, Databases, Python
Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia
Projects: iRhythmics, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis
Institutions: University of Rostock

Roles: PhD Student
Expertise: AI, Bioinformatics, RNA-Seq, Data integration, Transcriptomics
Projects: WG Infrastructure for Translational Research, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"
Institutions: University Medical Center Göttingen

Expertise: Data Management, Python, Bioinformatics, Databases, R, Data integration, Java, standards, Programming
Tools: Data Management, Java, Bioinformatics, Databases, Data integration, R, Python
Student (M.Sc. Medical Informatics) @ Georg-August-University Göttingen
Research Associate @ Department of Medical Informatics, University Medical Center Göttingen
Institutions: Latvia University of Agriculture
Roles: Postdoc
Expertise: Python, Mathematical modelling, Systems Biology, Dynamic modelling
Tools: SBML, Computational Systems Biology, constraint-based modeling, Python, Copasi, COBRA toolbox, cobrapy toolbox
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://imc.zih.tu-dresden.de/wiki/morpheus/) and is collaborating with experimental labs on questions of tissue morphogenesis and regeneration.
Projects: OXYMOD
Institutions: Norwegian University of Science and Technology

Roles: PhD Student
Expertise: protein NMR, lytic polysaccharide monooxygenases
Tools: NMR, Python, Molecular Biology, Biochemistry and protein analysis
Roles: Postdoc
Expertise: Programming, Dynamic modelling, parameter estimation, Biochemistry, Metabolomics, Data integration
Tools: AMICI, c++, PESTO, parameter estimation, Python
Projects: FAIRDOM user meeting
Institutions: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)
Expertise: Data Management, Databases, gene clusters, Python, RNA-Seq, Perl, Bioinformatics, R, secondary metabolites
Projects: COMBINE Multicellular Modelling
Institutions: Indiana University Bloomington

Expertise: Mathematical modelling, Python, Data Management, standards, Software Engineering, c++
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)

Expertise: Dynamic modelling, standards, Databases, Neuroscience, Mathematical modelling, NeuroML
Projects: DigiSal, GenoSysFat, SAFE-Aqua, Unlock
Institutions: Wageningen University & Research

Roles: PhD Student
Expertise: semantics, Python, Databases, Microbiology, Software Engineering, Java, Genetics, R, Data Management, Genomics
Expertise: genome-scale modeling, Kinetic modelling, Software Engineering, SBML, Python, Metabolic Control Analaysis, standards, Biochemistry, constraint-based modelling
Tools: Web services, FBA, SBML, metabolic network visualization, kinetic modeling, SED-ML, libSBML, F-A-M-E, PySCeS, CBMPy, Python, JWS Online
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
Expertise: Data Management, Python, Molecular Biology, Databases, Java, Bioinformatics, Data integration
Tools: Data Management
Computational Biologist
Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, WURSynBio
Institutions: Wageningen University & Research

Roles: PhD Student
Expertise: Molecular Biology, Bioinformatics, Dynamic modelling, R, Systems Biology, Python, pathogen host interaction, Agent-based modelling, Java
Tools: Copasi, R, libRoadrunner, semantic web, Python
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
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

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)
Expertise: computational structural biology
Tools: Molecular Dynamics, Data Science, Python, Data Management, web development, Databases, Ruby on Rails
Research associate at HITS, software developer
Projects: FAIRDOM
Institutions: ETH Zurich & Basel / The Scientific IT Services (SIS) division
Expertise: Software Engineering, distributed systems, Scientific Computing, Databases
Tools: High Performance Computing, Java, Statistics, Python, SQL
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.
Projects: FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, FAIRDOM user meeting
Institutions: University of Zürich, ETH Zurich, Manchester Centre for Integrative Systems Biology, University of Manchester
Expertise: Bioinformatics, Proteomics, Genomics
Tools: Perl, Python, Matlab, Computational Systems Biology, Microarray analysis, Data Management
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
Expertise: ODE modelling of biological interaction network, Bioinformatics
Tools: Python, bash, c++, standard bioinformatic tools, Java
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: School of Computer Science, University of Manchester, Manchester Centre for Integrative Systems Biology, University of Manchester

Roles: Postdoc
Expertise: Data Management, Stoichiometric modelling, Kinetic modelling, metabolic networks, Systems Biology, Metabolic Engineering
Tools: COBRA toolbox, Matlab, Python, Copasi
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
Expertise: Data Management, Bioinformatics
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
Expertise: Mathematical modelling
Tools: SubtiWiki, Python, Computational and theoretical biology, Bioinformatics
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
Expertise: Statistical Physics, Mathematical modelling
Tools: fortran, stochastic methods, Stochastic models, Mathematica, Matlab, Python
I am a phd student working on statistical physics and complex systems and applying concepts from these fields to biology.
Assay: _A_05_BUSCO
Short Name: 05_BUSCO
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/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar, /transfer/transfer.zip
Assay: _A_02.7_VecScreen
Short Name: 02.7_VecScreen
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/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum, Potato virus Y
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl
Assay: _A_02.3_InterProScan
Short Name: 02.3_InterProScan
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/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd
Assay: _A_02.1_BUSCO
Short Name: 02.1_BUSCO
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/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar
Assay: _A_03_BUSCO_1_3cvs-gffmerged
Short Name: 03_BUSCO_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: BUSCO on pantranscriptome
Description: BUSCO on pantranscriptome
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar
Assay: _A_04-MSA
Short Name: 04-MSA
Assay Class: DRY
Assay Type: MSA
Title: Multiple sequence alignment, pantranscriptomes' paralogue clusters
Description: Multiple sequence alignment, pantranscriptomes' paralogue clusters
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Contributor: Maja Zagorscak
Biological problem addressed: Multiple sequence alignment
Snapshots: Snapshot 1
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/D_P_R_g.tar.gz, /input/selected_4_wc.tar.gz, /other/Figure5.pdf, /output/output.tar, /reports/Figure4.pdf/, /reports/Merged.aa.html, /reports/SupplementaryFigure3.pdf, /reports/stPanTr_geneCount_paralogue-clusters.tiff, /scripts/scripts.tar, /testSet/testSet.tar
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.
Contributor: Gudrun Gygli
Biological problem addressed: various analyses of molecular dynamics simulations
Snapshots: No snapshots
Investigation: 1 hidden item
Study: Simulation Foundry for Methanol-Water Mixtures
Organisms: No organisms
Models: No Models
SOPs: ANALYSIS_1.5
Data files: No Data files
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.
Contributor: Gudrun Gygli
Assay type: Molecular Dynamics
Technology type: All-Atom
Snapshots: No snapshots
Investigation: 1 hidden item
Study: Simulation Foundry for Methanol-Water Mixtures
Organisms: No organisms
SOPs: SIMULATIONS_V1.5
Data files: No Data files
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.
Contributor: Gudrun Gygli
Assay type: Instructions
Technology type: Technical Computer Installation
Snapshots: No snapshots
Investigation: 1 hidden item
Study: Simulation Foundry for Methanol-Water Mixtures
Organisms: No organisms
SOPs: No SOPs
Data files: Installation Instructions
This is a collection of data that have been used to analyse data on deep eutectic solvent mixtures of choline chloride:glycerol:water.
Investigation: Deep Eutectic Solvents
Study: Choline chloride:glycerol:water mixtures in CML
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: CML files, CSV data, Python scripts for CML
_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA
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
Contributor: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Analysis Version 1.5
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
Contributor: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Simulation Version 1.5
Abstract (Expand)
Authors: Marko Petek, Maja Zagorscak, Ziva Ramsak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll Rius, Kristina Gruden
Date Published: No date defined
Journal: Not specified
DOI: 10.1101/845818
Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA
Creator: Maja Zagorscak
Contributor: Maja Zagorscak
Scripts and Input Files for Analysis V1.5
Creator: Gudrun Gygli
Contributor: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Analysis Version 1.5
Scripts and Input Files for Simulation V1.5
Creator: Gudrun Gygli
Contributor: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Simulation Version 1.5