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:

ChIP-seq peak profile
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

Linear Shifted Mode
Nonlinear Model
SDE model

Creasemarks analysis

Import formats
BED format (*.bed)
BioUML format(*.dml)
EMBL format (*.embl)
Fasta format (*.fasta)
Fastq format (*.fastq)
GenBank format (*.gb)
General Feature Format (*.gff)
Generic file
SDF file
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

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

Correlation Analysis
Fold-Change calculation
Hypergeometric analysis
Meta analysis
Polynomial Regression analysis
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