Tools

Many Hundreds of Software Tools


BioDatomics  is a unique system built on the BioUML platform and is specifically to both integrate many existing software technologies and methods, but also built in an open-source structure that is designed to make use of plug-ins. The concerted efforts of many researchers have resulted in a huge array of software tools available in the bio-research field; unfortunately the majority of these tools although open-source, are Command Line Interface (CLI) scripts and are not easy to use, and even harder to use in collaboration with other scripts. 

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Our programmers at BioDatomics have made it possible to very rapidly port these CLI scripts to the BioUML platform so that users can enjoy our dashboard not only to manage these scripts, but to allow the data to be used in different models and visual representations, in the same way as the tools integral to BioUML allow.  This means that anyone who can produce a script for their specific model can have it quickly ported into BioUMLin order to be able to run the scripts and also apply the functionality of BioDatomics to the script results. There are over 100 tools pre-built into BioDatomics and about 300+ third party add-on tools that have already been ported into the platform. This number is ever on the increase and as we progress we expect to be the the most comprehensive  integrated bioinformatics platform available anywhere in the world.

Below is a summary of the most popular tools and uses for this versatile platform:


BSA
• Bowtie
• ChIP-seq peak profile
• ChIPHorde
• ChIPMunk
• Compare site models
• Create IPS model
• Create Match model
• Create weight matrix model
• Gene set to track
• IPS motif discovery
• Matrices to molecules
• Motif quality analysis
• Process track
• Run MACS 1_3_7 on ChiP-Seq
• Run MACS 1_4_0 on ChiP-Seq
• SNP matching
• Search sites on gene set
• Site search analysis
• Site search result optimization
• Site search summary
• Track to gene set

General Data Processing and Manipulation
• Affymetrix normalization
• Agilent normalization
• Annotate table
• CRC Analysis
• Cluster analysis by K-means
• Convert table
• Create folder
• Enrichment analysis
• Filter table
• Functional classification
• Illumina normalization
• Join multiple tables
• Join table
• PASS analysis
• Select table columns


GeneModels
• Linear Shifted Mode
• Nonlinear Model
• SDE model

Creasemarks
• Creasemarks analysis








Import formats
• BED format (*.bed)
• BioUML format(*.dml)
• CellML
• EMBL format (*.embl)
• Fasta format (*.fasta)
• Fastq format (*.fastq)
• GenBank format (*.gb)
• General Feature Format (*.gff)
• Generic file
• BML
• BML(CellDesigner)
• SDF file
• SIF
• Tab separated file
• Text output file generated by R (.Routput)
• Upload from FTP
• Wiggle format (*.wig)
• ZIP-archive (*.zip)

Model Reduction
• Fluxes Analysis
• Quasi Steady State Analysis
• Reactions Analysis
• Steady State
• Stoichiometric Matrix


Molecular Networks
• Add expression values
• Cluster by shortest path
• Effector search
• Extend network
• Extend network by Transpath
• Regulator search
• Save hits
• Save network
• Visualize results


Optimization
• Adaptive simulated annealing
• Cellular genetic algorithm
• Evolution strategy (SRES)
• GLBSOLVE
• Particle swarm optimization
• Quadratic Hill-climbing

Statistics
• Correlation Analysis
• Fold-Change calculation
• Hypergeometric analysis
• Meta analysis
• Polynomial Regression analysis
•      Up and Down Identification
•      GALAXY Methods