GMOD tools: JBrowse, WebApollo, InterMine. Generic Model Organism Database Chado schema of relational databases.
Sequence analysis software (Blast, MEME-MAST, ClustalW, T-Coffee, HMMER, HHsearch.) Molecular structures visualization software (PyMOL, VMD, Rasmol, Dino, SPDBV) Molecular dynamics (NAMD) Molecular interactions (Mint, Osprey) Genomics: Maker, FastQC, ALLPATHS-LG, Circos, GeneMark, QIIME, Galaxy etcĭatabases: Relational: PostgreSQL & MySQL. R (also Shiny), Python, Perl, Unix shell scripts, HTML, CSS (Bootstrap), Javascript (AngularJS, Node.js), Ruby on Rails, PHP, Matlab, C/C++, Java. Pipeline/Workflow: Work Definition Language (WDL) Cromwell Virtual Computing: Docker, Vagrant.Ĭloud Computing: Google Cloud Platform (GCP) AWS Azure Operating Systems: Unix/Linux and Mac OS X.
PreLysCar (Predictor of Lysine Carboxylation), also available as a tool in the suite of structural biology programs CCP4ībTM-ST (beta-barrel TransMembrane Search Tool). MIDTOD: Metabolite Identification Through Orthogonal Datasets ( under development). TB OMICS EXPLORER: Multi-OMICS profiling of primary macrophages during Mycobacterium tuberculosis (TB) infection (part of this publication) R package: MotrpacBicQC: Primary and Secondary QC/QA analysis of datasets generated by the Metabolomic and Proteomic Chemical Analysis Sites (CAS) of the Molecular Transducer of Physical Activity Consortium (MoTrPAC)ĬAS to BIC Data Transfer QC Monitor: QC monitor tool that reports in real time datasets submitted and processed by the MoTrPAC Bioinformatics CenterīioNeNa (the FluOMICS bioNetwork Navigator): a systems biology tool to explore large-scale datasets Check the Github repo and the Bioconductor page. R package: artMS: Analytical R Tools for Mass Spectrometry. CloudProteo is currently being integretad as part of the tool omicsPipelines along numerous genomics pipelines (rna-seq, dna sequencing)
I have led/developed the following tools:ĬloudProteo: proteomics module for running proteomics pipelines on the cloud.
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