Projects

Data Science Meetups and Events

HackyHour

Date: Every 4^th Thursday of the month at 5pm
Website: https://hackyhour.github.io/Wuerzburg
Pad: https://go.uniwue.de/hackyhour-pad

Data Dojo

Date: Every 2^nd Thursday of the month at 6pm
Website: https://ddojo.github.io
Pad: https://go.uniwue.de/ddojo-pad

Data Crunch Cup Würzburg

Date: April (before the summer semester starts)
Website: https://dccw.de

Software Carpentry Workshops

Website: https://software-carpentry.org/
Local Chapter: https://github.com/swcarpentry-wuerzburg

Wue-RSE - Würzburg Research Software Engineers

de-RSE: https://de-rse.org
Local Chapter: https://de-rse.org/chapter/wue

Data Analytics Tools

misas - Model Interpretation through Sensitivity Analysis for Segmentation

Repo: https://github.com/chfc-cmi/misas
Docs: https://chfc-cmi.github.io/misas/`
Paper:

TBro - Transcriptome Browser

Idea: visualization and management of de novo transcriptomes
Online: https://tbro.carnivorom.com/
Repo: https://github.com/TBroTeam/TBro
Paper:

FENNEC - Functional Exploration of Natural Networks and Ecological Communities

Online: https://fennec.molecular.eco
Repo: https://github.com/molbiodiv/fennec
Docs: https://fennec.readthedocs.io/
Paper:

AliTV - Alignment Toolbox and Visualization

Online: https://alitvteam.github.io/AliTV/d3/AliTV.html
Repo: https://github.com/AliTVTeam/AliTV
Docs: https://alitv.readthedocs.io/en/latest
Paper:

bcgTree - Bacterial Core Genome Tree

Repo: https://github.com/molbiodiv/bcgTree
Paper:

bcdatabaser - Barcode Database Builder

Online: https://bcdatabaser.molecular.eco
Repo: https://github.com/molbiodiv/bcdatabaser
Paper:

chloroExtractor - Chloroplast Genome Extractor

Repo: https://github.com/chloroExtractorTeam/chloroExtractor
Paper:
Benchmark:

biojs-io-biom - Biological Observation Matrix Format in JavaScript

Repo: https://github.com/https://github.com/molbiodiv/biojs-io-biom/
Online: https://biomcs.iimog.org
Paper:

ITS2 Database Update - Internal Transcribed Spacer 2 Database Update

Online: http://its2.bioapps.biozentrum.uni-wuerzburg.de/
Paper:

Highlight Papers

Novel integrative elements and genomic plasticity in ocean ecosystems

Repo: https://github.com/thackl/pro-tycheposons
Paper:

Deep learning-based cardiac cine segmentation: Transfer learning application to 7T ultrahigh-field MRI

Repo: https://github.com/chfc-cmi/cmr-seg-tl
Data:
Paper:

Pollen Metabarcoding

Image Credit: NASA/Goddard Space Flight Center , Source

Repo: https://github.com/molbiodiv/meta-barcoding-dual-indexing
Evaluation Paper: - Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples
Dual-Indexing Paper: - Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach

Venus Flytrap - Dionaea muscipula - Genome and Transcriptome

Image: Public Domain, Source

Transcriptome Browser: https://tbro.carnivorom.com
Transcriptome Paper: - Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
Genome Paper: - Genomes of the Venus flytrap and close relatives unveil the roots of plant carnivory

Open Traits Network

OpenTraits Network: https://opentraits.org/
Network Paper: - Open Science principles for accelerating trait-based science across the Tree of Life
Ten Rules Paper: - Ten (mostly) simple rules to future-proof trait data in ecological and evolutionary sciences

Fun and Hobby Projects

X Game Manager (App)

Repo: https://github.com/iimog/x-game-master
Google Play: https://play.google.com/store/apps/details?id=org.iimog.xapp

Hot Wire

X Party Game

Repo: https://github.com/iimog/x-party-game

Minor Contributions

gggenomes - A ggplot2 Extension for Plotting Genomic Information

Repo: https://github.com/thackl/gggenomes
Docs: https://thackl.github.io/gggenomes/

permGWAS - Permutation-based Genome-wide Association Studies

Repo: https://github.com/grimmlab/permGWAS
Paper:

NixOS packages

Repo: https://github.com/NixOS/nixpkgs/
Website: https://nixos.org/
Maintainer for: dcmtk, hmmer, seaview