Well rounded biologist/biotechnologist/biochemist/enzymologist/bioinformatician/computational biologist.
Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia
Student (M.Sc. Medical Informatics) @ Georg-August-University Göttingen
Research Associate @ Department of Medical Informatics, University Medical Center Göttingen
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://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
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: 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
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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)
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,
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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: School of Computer Science, University of Manchester, 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
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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.
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
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
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
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
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
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
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
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
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
This is a collection of data that have been used to analyse data on deep eutectic solvent mixtures of choline chloride:glycerol:water.
Download_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
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
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
_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
Scripts and Input Files for Simulation V1.5
Creator: Gudrun Gygli
Contributor: Gudrun Gygli
