https://orcid.org/0000-0001-9119-1778Well rounded biologist/biotechnologist/biochemist/enzymologist/bioinformatician/computational biologist.
Research scientist in multi-Omics, molecular (cell)biology and bioinformatics.
Projects: ICYSB 2015 - International Practical Course in Systems Biology
Institutions: University of Tübingen
Trained as a Computer Scientist at the University of Jena, Germany, my interests drifted more and more towards "computing life" during my PhD at Simon Fraser University and the University of British Columbia, Canada. On one hand, that term captures that I got fascinated by the idea to understand life as a form of computation and to describe, reprogram, and reassemble parts of cells as described in many brilliant experiments from a spectrum of disciplines ranging from DNA computing to Synthetic
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BUSCO post filtering and reassignment
TransRate post filtering and reassignment
Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters
Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
DIAMOND on raw (initial) tr2aacds output, both .cds and .tr; including lost and found
VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output
TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based
mapping reads back to initial evigene .tr output using STAR to check the percentage of reads that map
potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations
InterProScan on tr2aacds output
assembly contribution count, input/output tr2aacds
Contributor: Maja Zagorscak
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
BUSCO on initial assemblies -- tr2aacds output
EvidentialGene tr2aacds.pl VERSION 2016.07.11
See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html
tr2aacds on cv rep and gffmerged
paralogue clusters on pantranscriptome
BUSCO on pantranscriptome
Multiple sequence alignment, pantranscriptomes paralogue clusters
Contributor: Maja Zagorscak
Biological problem addressed: Multiple sequence alignment
Snapshots: No snapshots
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
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
_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
