2011 February
- HMDFinder – Methylation Prediction in Human Genome
- BIOSAP 0.1.7 – Generate Oligos for the Inkjet Arrayer
- GeneXplorer 0.11 – Microarray Data Web Browser
- LuceGene 1.4 – Search System for Genome & Bioinformatic Databases
- GO Term Finder 0.86 – Gene Ontology Term Finder
- Flash GViewer 0.5 – Customizable Flash Movie to Display Chromosome in Genome
- CMap 1.01 – View Comparisons of Genetic & Physical Maps
- blastGraphic 0.02 – BLAST Graphic Viewer
- Indelign 2.0.4 – Probabilistically Annotating Indels in Multiple Alignments
- D2Z 0.1 – Alignment Free Comparison of Regulatory Sequences
- EMMA 1.1 – Prediction & Alignment of Cis-regulatory Modules
- Swan v6 – Motif Scanning
- CMfinder 1.0 – Predict RNA Motifs in Unaligned Sequences
- YMF 3.0 /FindExplanators 1.1.3 – Finds Short Motifs in DNA Sequences
- FootPrinter 2.1 / MicroFootPrinter – Phylogenetic Footprinting
- PGT 0.42 – Projection Genomics Toolkit
- Mandala 1.1.1 – Generate Seed Designs for Seeded Alignment Algorithms
- Dapple 0.88pre4 – DNA Microarrays Image Analysis
- MSS 1.0 – Finding all Maximal Scoring Subsequences
- paircomp 1.0 – Ungapped Comparisons of Two Sequences
- FamilyRelations II 20070330 – Comparative Sequence Analysis
- VISTA Browser 2.2.47 – Visualize Alignments
- mVISTA – Compare Sequences & Visualize Alignments with Annotation Information
- ROVER 20050711 – Find Relatively Overrepresented Motifs in DNA Sequences
- GLAM / AGLAM 2.1 – Gapless Local Alignment of Multiple Sequences
- Cister – Find Motif Clusters in DNA Sequences
- COMET – Cluster Of Motifs E-value Tool
- Cluster-Trainer 20071204 – Estimates Optimal Motif Weights for Cluster-Buster
- Cluster-Buster 20100219 – Find Dense Clusters of Motifs in Nucleotide Sequences
- ICSF – Identification of Conserved Structural Features
- REPFIND 20040309 – Find Clustered, Exact Repeats in Nucleotide Sequences
- MOMA – Minimal Perturbation Analysis
- Bio-SPICE Dashboard 7.0 – Viological Simulation Program for Intra- & Inter-Cellular Evaluation
- Pointillist 2.1.2 – MATLAB Codes of Iterative Framework for Biological Modeling
- ISBJava 2.4.4 – Java library for Research in Computational Biology
- Dizzy 1.11.4 – Chemical Kinetics Stochastic Simulation
- Cellware 3.0.1 – Modeling & Simulation Tool for Modeling Cellular Transactions
- SSC 0.6 – Stochastic Simulation Compiler
- NFsim – Biochemical Reaction Simulator
- little b 1.6.0 – Language to Build Mathematical Models of Complex System
- E-Cell 3D demo – 3D Cell Simulation
- BioSPI – SIMULATION OF BIOCHEMICAL PROCESSES
- CHARON 1.0 – Language for Modular Specification of Interacting Hybrid System
- SigTran 3.0.4 – Cell Signaling Simulation Software
- BALSA – Cell Systems Modeling Environment
- OpenAlea 0.9 – Plant Modeling Environment
- modelMaGe 1.0 beta – Automatic Model Management & Generation
- Moleculizer 1.1.3 – Cellular Reaction Network Stochastic Simulator
- Monod/Desktop 1.535 – Server/Client Knowledge Management & Collaboration
- SpectFit 2.0 – Non-linear Data Fitting
- HillSim 1.0 – Signaling System Analyzer
- STOCHSIM 1.4 – Stochastic Simulator for Biochemical Reactions
- BCT 4.4 – Bacterial Chemotaxis Modelling & Simulator
- NIH Image 1.63 – Image Processing & Analysis for the Macintosh
- DINO 0.9.4 – Structural Biology Data 3D Visualization
- VisBio 3.40rc1 – Biological Visualization Tool
- 3D Nuclei Detector Matlab Toolbox 0.1 – Identify Nuclei Centroid Locations
- BQJavaLib 0.1 – Java Library for Matlab to Direct Access to the Bisque DataBase System.
- BQMatlabToolbox 0.1 – Direct Access to the Bisque DataBase System
- ITCN 1.6 – ImageJ Plugin for Image-based Tool for Counting Nuclei
- BQBisqueJ 0.1 – ImageJ plugin for Bisque DataBase System
- bioView 1.1.18 – Visualize EM, Confocal, etc. Biology Imagery
- Digital Notebook 1.2.28 – Image Management & Annotation
- Bisque 0.4.9 – Platform for Bioimage Analysis & Management
- Segtrack – C++ & MatLab Library for Image Tracking & Segmentation
- Sassign 2 – C++ & MatLab Library for Image Target Tracking
- Costanza 1.0 – ImageJ Plugin for Image Segmentation & Analyzing Stacks
- CLSM Tools 20080903 – MATLAB Library for Nuclear Segmentation & Lineage Analysis
- SME 1.8 – Sigmoid Model Explorer
- SBML Converters 20100413 – Conversions to & from SBML
- MathSBML 2.10 – working with SBML in Mathematica
- KEGG2SBML 1.5.0 – Convert KEGG Pathway Database to SBML
- MICE 1.4 – Mouse Information & Classification Entity
- FCSM – Frozen Cell Stock Monitor
- SBML2SMW 1.0 – Extract Celldesigner Model to Semantic Mediawiki
- Payao Uploader 1.0 – CellDesigner Plugin to Upload Model to Payao
- SBMLsqueezer 1.3 – Generate Kinetic Equations for Biochemical Networks
- PathwayAccess 1.0 – CellDesigner Plugins for Pathway Databases
- Merge Models 1.03 – CellDesigner Plugin to Merge Models
- Import Notes 1.1 – CellDesigner Plugin, Import Notes Data from CSV File
- Ometer 0.6 – Multivariate Data Analysis
- Gepasi 3.30 – Biochemical Kinetics Simulation
- CERVUS 3.0.3 – Parentage Analysis
- Exceltranspose – Convert Excel File to Genetic Software Fomat File
- ALFmap 1.22 – Convert ALF Format File into Bitmap File
- ComBin 1.1 – Ultra-dense Linkage Maps Construction
- LCMT – Multiple Genetic Markers Association test
- XWXW – Linkage Analysis of Quantitative Traits
- ResqMi 1.2.1 – Affymetrix Resequencing Microarray Data Analysis
- ProbeWithO 0.9.0 – Use Small Probe Contact Dots Within O
- PDBCNS 2.0 – Interconvert Atom Names between PDB & CNS formats
- MapVol 1.1 – Awk Script to Assign Volume by Atom
- COCAS 2.4 – ChIP on Chip Analysis Suite
- VIZARD 1.2 – Affymetrix GeneChip® Data Analysis & Visualization
- ScoreDotsAtAtom 1.0 – Bookkeep All-atom Contact Dot
- Autobondrot 2.0 – Generate Multiple Molecular Conformation
- NAContacts 2.5 – Write Contact Information between Nucleic Acid Bases
- Flipkin 2.4 – Script to Make the Kinemages
- ClashList 1.1 – Build Lists of van der Waals Clashes from PDB file
- ClashScore 1.1 – R Script for VTF Percentile Plot
- Picky 2.2 – Optimal Oligonucleotide Design & Analysis
- BndLst 1.6 – List Covalent & H-bonded Neighboring Atoms
- AtVol 1.2 – Atomic Volume Calculation
- Cluster 1.3 – Build Collections of Interacting Items
- Kin2Dcont 1.8 & Kin3Dcont 1.12 – Produce Molecule Contour Map
- Dangle 0.63 – Read PDB File & Generate Geometric Measurement Table
- Dang 1.8 – Read PDB File & Generate Geometric Measurement Table
- Correlate 1.03 – Integrative Analysis of 2 Genomic Data Sets
- PermutMatrix 1.9.3 – Microarray Data Cluster & Seriation Analysis
- Remediator 1.60 – Convert PDB Files between PDBv2.3 & PDBv3.2 Formats
- Suitename 0.3 – RNA Conformer
- RNABC 1.11 – RNA Backbone Correction
- RDCvis 1.02 – Residual Dipolar Coupling Visualizer
- KinImmerse 0.5 – Translate Kinemage Files into Software for Virtual Environment
- Prekin 6.51 – Prepares Kinemages Files from PDB-format Files
- ENIGMA 1.1 – Extract Gene Expression Modules from Perturbational Microarray Data
- GenePublisher 1.03 – Analysis of DNA Microarray Data
- OligoWiz 2.2.0 – Design oligonucleotides for DNA microarrays
- Mage 6.47 – Kinemage File 3D Display
- ORTEP-III 1.03 – Crystal Structure Illustration
- Array Tools 3.3 – Dictyostelium Discoideum Microarray Data Analysis
- MAGIC Tool 2.1 – MicroArray Genome Imaging & Clustering Tool
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