Software

Bioinformatics, data analysis and other software licenses and codes

Major Bioinformatics packages

• EMBOSS
• BLAST
• CLUSTAL
• Phred/Phrap/Consed
• CAP3
• Perl/Bioperl
• R
• ARB
• Phylip
• PAUP
• MUMMER
• HMMER

Commercial software licenses

Multiple Matlab licenses with all toolboxes and add-ons, Microsoft Windows and Office for all PC Workstations, Microsoft Visual C++, Microsoft Visio, Adobe Acrobat, Reference Manager, f Borland IDE (JBuilder, C++ Builder, Delphi, etc), Hugin Educational, LINGO Optimization package, JMP, LogXact, Mathematica, Mathtype, MetaAnalysis, Netica, nQuery Advisor, SAS, See5, SOLAS, S-Plus, SPSS, StatXact, multiple licenses of backup, archiving, and media (DVD,CD) recording software.

Installed publicly available software packages

Borland Interbase Client and Server; WRQ Reflection; OpenSSH Client and Server; Putty SSH
Client; WinSCP2; WinCVS; VNC Clinet and Server; mySQL; GhostScript; TCL; Cygwin; FAR
Manager; WinRAR; WinZIP; Genie; MikTex; Mcafee antivirus packages; WEKA; Eisen
Clustering Software; BayesBuilder; BNJ; BNSoftware; C4.5 implementations; a number of SVM
implementations (including regression and multicategory classification);
CLABROC/ROCIT/LABROC; JavaBayes; LIBB; PEPI; RscorePlus; Smile; MRBN; TETRAD
3 and 4; BNT for Matlab; Classification Toolbox for Matlab; GraphLayout for Matlab; Isomap
for Matlab; MatlabMPI Toolbox; mySQL Matlab Toolbox, Parallelization Toolkit for Matlab;
Statbox for Matlab; Strauss Statistical toolbox for Matlab; Tomlab for Matlab; Econometric
Toolbox for Matlab; UCSD_Garch for Matlab; EPS Toolkit 2 for Matlab; etc.

Custom and proprietary software implementations

• GEMS and FAST-AIMS systems for automated analysis of gene expression and massspectrometry data
• EBM-Search information retrieval system toolkit for PubMed and ISI parsing toolkit for text
  pre-processing and text categorization model building
• Various classification and regression algorithms – KNN, Naïve Bayes, Naïve Bayes for
  text, AdaBoost, Decision Trees (interface to See5), NN and Perceptron (interface to Matlab NN
  Toolbox), Random Forests, SVMs (interface to a number of SVM implementations), etc.
• Local Causal Discovery Algorithms – GS, GSnPC, IAMB (regular, chunked, parallel chunked,
  and parallel fine grain), IAMBnPC, interIAMB, interIAMBnPC, KS, LCD2, MMMB,
  MMMBnPC, HITON_PC, HITON, MMPC, RFE, UAF, and SVMFS
• Global Causal Discovery Algorithms – PC, TPDA, MMBN, and SCA
• High-quality implementations of and/or interfaces to over 30 filter and wrapper
  biomarker selection algorithms and variants (e.g., LARS, LARS-EN, 0-norm SVM, RFE, GAKNN,
  Spider toolkit, UAF, PCA, RF, etc.)
• Software for Relative Blocking Analysis
• Experiment Logging System
• Standalone Demo of DSL Algorithms
• Causal Explorer toolbox of local and global causal discovery and variable selection algorithms
  (includes high-quality implementations of GS, IAMB (regular and parallel chunked), interIAMB,
  IAMBnPC, interIAMBnPC, KS, PC, TPDA, LCD2, and SCA algorithms)
• BN file parsers (for Hugin and LIBB)
• BN Tiling Toolkit (distributed as a part of Causal Explorer) high-fidelity network resimulation
  code
• Various scripts for experimental design (nested stratified cross-validation, etc)
• Data preparation tools: discretization algorithms, normalization scripts, imputation algorithms
• Graph tools and algorithms – manipulations with adjacency matrix, search algorithms,
  maximum flow algorithm, min vertex set algorithm, transitive closure
• Implementations of various performance (loss function) metrics
• Interface to ROCIT/CLABROC/LABROC
• Interface to TETRAD 3
• Efficient implementations of many statistical, probabilistic, and information theory routines
• Interface to multiclass SVM implementations.