Miscellaneous
- Planform 2.2.8 – software of Graph-encoded Planarian Regenerative Experiments
- irootlab 20130219 – MATLAB toolbox for Vibrational Spectroscopy
- SPEX2 – Automated Concise Extraction of Spatial Gene Expression Patterns from Fly Embryo ISH Image
- SUMMON 1.8.10 – Visualization Prototyping and Scripting
- CummeRbund 2.0.0 – Exploration, Analysis and Visualization of Cufflinks high-throughput RNA-Seq data
- ChromHMM 1.06 – Chromatin State Discovery and Characterization
- PWIMS 2.3 – Proteomics Workflow and Information Management System
- SCUBA 1.0 – Single-cell Clustering Using Bifurcation Analysis
- MAnorm – Robust Model for Quantitative Comparison of ChIP-seq datasets
- HGNChelper 0.2.2 – Handy functions for working with HGNC Gene Symbols and Affymetrix probeset identifiers
- GT-Miner 1.28 – Visual Data Analysis and Mining Operation
- XYLab – XY Plotter for Multivariate Data
- jHeatmap – Create interactive Heatmaps on the Web
- SVGMap 1.5 – Image Browser for Experimental data
- Tclass – Tumor Classification System based on Gene Expression Profile
- SamCluster – Discovery of Sample Classes using Gene Expression Profile
- pPIC9 – Evaluation and Design for high-level Expression of Foreign Genes in pPIC9 Vector
- ManhattanPlotter – Create Manhattan Plots and qq plots from P-values obtained in Genomic Studies
- GoMiner Build328- Resource for Biological Interpretation of Genomic and Proteomic data
- Lichen / R.Lichen – Provide Network and Heat Map Visualization in web browsers
- Fastbreak – Structural Variant Detection in Genomic data
- DoDoMa – Analytical tool to Identify Transcription Factors with matching DNA Binding Domains
- Pubcrawl – Networks of Literature-based Semantic Distances with Protein Domain Interactions
- SPLASH – Structural Pattern Localization Analysis by Sequential Histograms
- DTWave 1.0 – Dynamic Time Warping for Spectrogram Alignment and AVErage Sequence Computation
- ARTO – Analysis of Replication Timing and Organization
- MonoClad – Find meaningful partitions using Semi-supervised Class Discovery
- TAP 1.8 – Calculate TAP and TAP-k to Evaluate Bioinformatics Retrieval Methods
- SeqCalc 1.0 – Portable software for Sequence Analysis
- RandSeq – Generate Multi-FASTA file following the Given Frequencies
- RaTrav 20130326 – Calculating Mean First Passage Times using Hill’s and Monte Carlo algorithms
- TFBphylo 1.0 – Evolution of Transcription Factor Binding events using Multi-species ChIP-Seq data
- Gimli 1.0.2 – Annotation of Biomedical Entity Names
- CORRECTOR 1.91 – High Throughput tool for the Mass Isotope Correction of GC-MS Flux Profiling experiments
- TagFinder 4.0 – Chromatography data preprocessing suite
- pro Fit 6.2.9 – Scientific Application for Non-linear Curve-fitting
- MascotDatfile 3.4.9 – java API for MS/MS search results by Mascot
- TASE 1.5.1 – Tag-counting and Analysis of Solexa Experiments
- FunSys 20120525 – Transcriptome and Proteome Analyzes for Prokaryotes
- OSIRIS 2.1 – Analysis of Multiplex DNA Profiles
- GEM 1.3 – Study Protein-DNA interaction using ChIP-Seq/ChIP-exo data
- L-Measure 5.0 – Extract quantitative Morphological Measurements from Neuronal Reconstructions
- LDA 1.6.1 – Lipid Data Analyzer
- OpenMS / TOPP / TOPPAS 1.10 – C++ Framework for Proteomics
- RefSeq 58 – NCBI Reference Sequence Database
- PAST 2.17c – PAlaeontological STatistics
- EMEN 2.2b3 / EMDash 2.2b5 – Object Oriented Database and Electronic Lab Notebook / Client Utilities
- SpliceGrapher 0.2.2 – Creat Splice Graphs from RNA-Seq data
- JCMS 4.6.0 – Colony Management System
- QUOSA 8.07.737 – Manage Scientific and Technical Documents
- Biobar 2.0.7 – Firefox Toolbar for Browsing Biological Data and Databases
- IRMa 1.31.1 – Validation of MS Peptides Identification
- MZmine 2.10 – Mass-Spectrometry Data Process
- ReaderFit 2.0.0.77 – Curve-Fitting Software for ELISA Analysis
- Labmatica 2.2.1 – Laboratory Information Management System
- SimLipid 3.50 – Characterize lipids using Data from MS, MS/MS and MSE
- SimGlycan 4.50 – Glycan & Glycopeptide MS/MS Data Analysis Tool
- CDK-Taverna 2.0.5.4 – Workflow Management System for Cheminformatics
- CDK 1.4.17 – Java Library for Structural Chemo- & Bioinformatics
- Maltcms 1.2.1 – Modular Application Toolkit for Chromatography Mass-Spectrometry
- Melting 5.1.0 – Compute Nucleic Acid Duplex Melting Temperature
- openBIS 8.04.5 – Managing Biological Information
- WellReader 3.0 – Analysis of Fluorescence and Luminescence Reporter Gene data
- Utopia Documents 2.2 – Tool for Interacting with the Scientific Literature
- MPA 1.0 – Multiple Peak Alignment
- FusionSeq 0.7.0 – Detect Chimeric Transcripts from Paired-end RNA-seq Experiments
- LabKey Server 12.3 – Organize, Analyze, and Share Biomedical Research data
- Pepline 2.0.1 – Mapping of MS/MS data to Genomic DNA Sequences
- myProMS 2.7.2 – Management, Validation and Interpretation of MS-based Proteomic data
- ade4 1.5-1 / ade4TkGUI 0.2-6 – Ecological Data Analysis
- FretTrace 1.0 – Maximum Likelihood Trajectories from Single-molecule FRET Experiments
- BioGene 1.3 – Information Tool for Biological Research for Iphone
- PAST 1.31 – Store & Archive Multiple Datestamped Snapshots of PDB
- papers 2.4.9 – Personal Library of Research
- CL!Psci 1.32 – Life Science Search Engine
- RefNavigator 2.5 – Search Scientific References and Generate Bibliographies
- OptiCount 201303 – Enumeration of Plankton and Particles
- ezFreezer 1.4.5 – Samples and Specimens Storage Management
- E1DS – Predict Enzyme Catalytic Site
- pUMA 1.11 – Handling the Genomics Projects Complexity
- Magallanes – Multi-Architecture Resources Discovering
- Oasys 1.0 – A Graphical Genomic Viewer for Omics Data
- Biowep – Workflow Enactment Portal for Bioinformatics
- FuncAssociate 2.0 – Gene Sets Characterizing & Functional Trend Analysis
- QUEXT – Find Relationships between Genes
- NEJI – Framework for Faster Biomedical Concept Recognition
- BioCRF 0.9 – Grammatical-Restrained HCRF tool for Bioinformatics applications
- GeneTerrain – Next-generation Panel Biomarker Discovery and Validation software
- BEIN 1.1.0 – Workflow Manager and Miniature LIMS system
- Anduril 1.2.15 – ANalysis of Data Using Rapid Integration of aLgorithms
- Piranha 1.2.0 – Peak-caller for CLIP- and RIP-Seq high-throughput Protein-RNA interaction data
- BATMAN 1.1.0 – Bayesian AuTomated Metabolite Analyser for NMR spectra
- Ibidas 0.1.23 – Integrated Database System for Biological Data
- Database Manager 2.1 – FASTA Database Manager
- MassXpert 3.4.0 – Polymer Chemistry Modelling & Simulation/Analysis of Mass Spectrometric Data
- CBT++ – Collection of C++ Classes to Computational Biology Applications
- BNFinder 2.0.2 – Bayesian Network Topology Inference
- mz2m 2.17 – Interpretation of Peptide Mass Spectra
- GCAligner 1.0 – Alignment of Chemical data obtained by Gas Chromatography
- MSI – Multiscale Systems Immunology
- Baescs 1.15 – Estimate Calibration Curves and unknown Concentrations in Immunoassays
- validate – Omics Validation Calculator
- CoreArray 1.0 – Developed Portable and Scalable Storage Technologies for Bioinformatic data
- TargetMine 20121115 – Data Warehouse for Candidate Gene Prioritisation and Target Discovery
- SeqSite 1.1.2 – ChIP-Seq Binding Site Identification
- SimGene 1.0.3 – Provide Gene and Transcript Cross Reference Information
- iCut DNA 2.5.0 – Search the Restriction Enzyme Database (REBASE) for Enzymes
- Nature Human Genome Special Edition 1.0
- Nature ENCODE 1.1 – Bring together the Results of the ENCODE project for iPad
- BioLegend CD Posters 1.4 / BioLegend Tools for iPad 1.4 – Information about Mouse and Human CD Molecules
- BioLegend ELISA 1.1 – ELISA Active Protocol
- Life Technologies Protocols 1.1.2 – Access to popular Applied Biosystems or Invitrogen product protocols
- An Array of Genetic Tools from Gene Link Inc. 1.2.1 – iPhone / iPad APP
- ColonyCount BETA – Assist Counting Bacterial Colonies on Agar Plates
- WIST 1.1 – The Workflow Information Storage Toolkit
- VDA 0.1 – Design Minimal Validation Dataset to allow Reliable Comparisons
- bioimage wip – BioImage Workflow Image Processing
- PhenoFam – Gene Set Enrichment Analysis in the Protein Domain Context
- chemViz – Cheminformatics Plugin for Cytoscape
- Exchanger 1.0 – Send files to a Bioinformatician and Receive analyses
- Bioinformatics Analysis Scripts
- LACS – Validate Protein NMR Chemical Shifts
- SCORER 2.0 – Distinguish Parallel Dimeric and Trimeric Coiled-coil Sequences
- StAR – Statistical Analysis of Receiver Operating Characteristic (ROC) Curves
- Sight 3.2.0 beta – Automatic running of Bioinformatical Tools on Remote Servers
- cb2bib 1.4.9 – Manage Bibliographic data in BibTeX Format
- Virusbanker 1.0 – MySQL database of Virus Sequences and Alignments
- MLPERCEP 2.0 – Multiple Layer Perceptron Implementation for the Biological Problems
- rcNet – Web Tool for Inferring Disease and Gene Set Association
- SMK 2011v4 – Mining Low-support Discriminative Patterns from Dense and High-dimensional Data
- MetaQuant 1.3.5 – Quantification of GC/MS based Metabolome data
- I, Librarian 2.9 – PDF manager for Scientific Articles
- GO2MSIG 20120814 – GO based GSEA Gene Set Generator
- DNASIZE – Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility
- BLOSpectrum 20050317 – Split BLOSUM Score into numbers of Biological Significance
- JPerl 200704 – Jamie’s Perl Scripts for Bioinformatics
- BACGrid 1.0 – BAC Data Processing Macro for MS Word
- BACMan 2.1 – Bacterial Artificial Chromosome Data Management
- LINNAEUS 2.0 – Species Name Recognition and Normalization software
- GETM 20100519 – Gene Expression Text Miner
- text2genome 0.4 – Extract DNA Sequences from Biomedical Text
- pubmed2ensembl – Link Publications in PubMed to Genes in Ensembl
- BioContext 1.0 – System for Extraction and Contextualization of Biomedical Events
- EcologIE PMCMiner 0.1 – Extract Information about Species Interactions from the Ecological Literature
- kernel-compute 1.0 – Profile-based Kernel Compute Package
- MaRIboES 2.1.0 – Metabolite and Reaction Inference based on Enzyme Specificities
- HATSEQ / HAT – Hypergeometric Analysis of Tiling-arrays and SEQuence data
- GiA Roots – Analysis of Plant Root system Architecture
- CASSys – Interactive Analysis of ChIP-seq data
- GeneVenn – Gene list Venn Diagram
- GeneCite 3.0 – High-throughput Literature and Pathway Mining
- Regression tree package – Implementation of Ensembles of Multiple output Regression Trees
- bioECS 1.0 – Biology Easy Cluster Search
- Gemvid 0.8c – Monitoring System for Rodents
- fs_kit 0.1 – Analysis of Force Spectra
- MetaGeneAlyse – Analysis of Gene Expression and Metabolite data
- SpecView 1.0 – Excel Spectrum Viewer
- Judi 1.0 – Data and Model Integration for Biology
- MetaFIND 0.8 – Java-based Metabolomics Analysis software
- PICA Browser 0.9 – Integrating and Exploring Multiple Connected Datasets
- MBRole – Enrichment Analysis of Metabolomic data
- ms-lims 7.7.7 – Mass Spectrometry based Proteomics Information Management System
- iRefWeb 4.1 – Consolidated Protein Interactions from many source DBs
- Reflect - Automated Annotation of Biochemical Terms in web pages
- OnTheFly 2.0 Beta – Automated Annotation of Biochemical Terms in PDF, Text and Microsoft Office documents
- PubNet – Publication Network Graph Utility
- XplorMed – Explore a bibliographic search in MEDLINE
- LSAT – Literature Support for Alternative Transcripts
- KAT – Gene Annotation from Scientific Literature
- metaTIGER – A Metabolic Evolution Resource
- BTL 3.4 – The Bioinformatics Template Library
- PentaPlot 20040723 – Illustration of Genome Mosaicism
- BioSVG 0.02 – Generate Scalable Vector Graphics (SVG) data for Biological objects
- BIOSEG 0.8 – Biological Interval type for PostgreSQL
- KEX 1.21 – A simple Knowledge EXtraction tool
- ABNER 1.5 – Molecular Biology Text Analysis
- Moara 1.0.6 – Extract & Normalize Gene and Protein Mentions
- SENT – Functional Interpretation tool based on Literature Analysis
- bioNMF 2.0 – Non-negative Matrix Factorization in biology
- Base Pad 1.0 – Base Sequence Editor
- Link3D 1.0.0 – Drug Discovery and Development
- iHOP – Information Hyperlinked over Proteins
- SNOW – Standard Nomenclature Wizard
- SEA – Serial Expression Analysis
- ARco 1.0 – Association Rules collaborative tool
- ABE 1.0 – Bioassay Analysis program
- SATuRNo – Supervised Prognostic Approach Through Regression Networks
- Cromwell 1.0 – The New Model Processor for Mass Spectrometry Data
- efron 1.1 – Estimate the p-value in support of a Hypothesis of Recombination
- Labux 0.1 – Open Source software for Laboratory Automation Control
- FastPval – Fast Two Stage P-value Computation Software
- SEMPPR 1.0.2 – Stochastic Evolutionary Model of Protein Production Rates
- COPS Benchmark 2009/6 – Interactive Analysis of Database Search Methods
- LGT3State 20081223 – Detect LGT (swapping) of two non-homologous Enzymes
- multi_mantel – Multiple Matrix Regression and Hypothesis testing
- skewers – Cheverud’s Random Skewers Method of Matrix Comparison
- exim – Compare Time-series Expression Profiles
- PuReD-MCL 20111130 – PubMed Document Clustering
- ChargeCzar 1.1.17 – Peptide Charge State Determination
- TAMEE 1.1 – Tissue Array Management and Evaluation Environment
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