Palmer Lab

Major tools that we develop include:

SequenceServer

• BLAST is the most commonly used bioinformatics tool. But setting it up for private data and using it is counter-intuitive. We developed SequenceServer to make BLAST easy to use.
• A Priyam, BJ Woodcroft, V Rai, A Munagala, I Moghul, F Ter, MA Gibbins, H Moon, G Leonard, W Rumpf, Y Wurm. 2015. Sequenceserver: a modern graphical user interface for custom BLAST databases. biorxiv doi: 10.1101/033142.
• http://github.com/wurmlab/sequenceserver

GeneValidator

• Tool to identify problematic gene predictions based on comparison with gene predictions in public databases. Funded by NESCent Google Summer of Code 2013.
• MA Dragan†, I Moghul†, A Priyam, C Bustos, Y Wurm. 2016. GeneValidator: identify problems with protein-coding gene predictions. Bioinformatics, 32:1559-1561.
• https://github.com/wurmlab/genevalidator

BioNode

• BioNode is Node.js JavaScript library for client and server side bioinformatics. Used in production. Development ongoing. Contributors welcome.
• http://bionode.io

oswitch

• Provides quick and simple Docker based virtual environments on Macs and compute clusters alike for reproducible bioinformatics. Funded by NERC Environmental 'omics (EOS) Cloud.
• https://github.com/wurmlab/oswitch

Afra

• BBSRC-funded tool for crowd-sourcing curation of gene predictions.
• http://github.com/wurmlab/afra
• Beta. Used in Bioinforatics MSc course at QMUL.

Transcript-genome consistency network

• TGNet is a Cytoscape-based tool for visualization and quality assessment of de novo genome assemblies. Specifically it facilitates rapid detection of inconsistencies between a genome assembly and an independently derived transcriptome assembly. Developed by Oksana Riba-Grognuz. Used for fire ant genome project.
• O Grognuz, L Keller, L Falquet, I Xenarios, Y Wurm. 2011. Visualization and quality assessment of de novo genome assemblies. Bioinformatics 27: 3425-3426.
• https://github.com/ksanao/TGNet

Fourmidable / antgenomes.org

• Community database centralizing genomic and transcriptomic sequence information for ants and related species (e.g., bees and wasps). Provides BLAST search and data download. Updated periodically with latest data and new tools.
• Y Wurm, P Uva, F Ricci, J Wang, S Jemielity, C Iseli, L Falquet, L Keller. 2009. Fourmidable: a database for ant genomics. BMC Genomics 10:5.

Approaches

We believe in Reproducible Research & Software Sustainability. When possible we respect style guides and use unit testing & continuous integration. We develop mostly in:

• ruby/bioruby when making pipelines, text & backends
• R for number crunching
• javascript/html/css for client-side stuff and some bioinformatics analysis pipelines
• But also use bash/python/perl when convenient or necessary...

But we love quick and dirty hacks too .