Abhishek Tiwari:Links

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=Programming=

Python and Biopython

 * Python Programming Language -- Official Website
 * BioPython -- Official Website
 * Penzilla.net's Python Tutorial  MPI on Python *****
 * Python course in Bioinformatics Pasteur Institute
 * Dave Kuhlman 's WebPage on Python
 * Python PLEAC - Programming Language Examples Alike Cookbook PLEAC
 * Python Documentation
 * An Introduction to Python --Guido van Rossum
 * Byte of Python
 * Introduction to Python -- Dave Kuhlman
 * Advanced Python Topics -- Dave Kuhlman
 * Programming for Bioinformatics in Python
 * Introduction to Programming using Python for Biologists at the Pasteur Institute
 * Python HOWTOs Regular Expression HOWTO
 * Python Programming Tutorial Richard G Baldwin
 * Beginning Python for Bioinformatics by Patrick O'Brien
 * A Beginner's Python Tutorial
 * Python Tutorials List and Links
 * Python:Choose Your GUI Toolkit
 * Building GUI Applications with PythonCard and PyCrust
 * Python Library Reference
 * Python Tutorial --Guido van Rossum
 * Biopython Tutorial and Cookbook --Jeff Chang, Brad Chapman, Iddo Friedberg
 * Python for Structural Bioinformatics
 * Python: A Programming Language for Software Integration and Development
 * Bioinformatics (Programming Python for Bioinformatics)
 * Python in Bioinformatics and Chemical Informatics
 * Beginning Python for Bioinformatics
 * Using Python to solve problems in bioinformatics
 * SciPy Scientific Tools for Python
 * NumPy N-dimensional Array manipulations
 * Topical Software Links categorized by scientific discipline or computational topic
 * Open Source Free Python CGI Scripts for Molecular Biology and Bioinformatics
 * AstraZeneca Uses Python for Collaborative Drug Discovery
 * Dive Into Python
 * Other Python links

Perl and BioPerl

 * Perl.org use Perl;
 * Perl.com
 * ActivePerl
 * Perl Paraphernalia by Mark Jason Dominus Coping with Scoping  Higher-Order Perl
 * Perl Circus Regex  Hashes
 * perlmeme.org HOWTO  TUTORIALs  index Regular expressions
 * Comprehensive Perl Archive Network
 * Perl PLEAC - Programming Language Examples Alike Cookbook PLEAC
 * BioPerl
 * Perl in a Nutshell
 * Learning Perl
 * Learning Perl on Win32
 * Programming Perl
 * Advanced Perl Programming
 * Perl for System Administration
 * Perl Cookbook
 * The Perl You Need to Know -Aaron Weiss -Stas Bekman
 * CGI Programming with Perl
 * CGI Programming on the World Wide Web
 * CGI Programming 101: Learn CGI Today!
 * CGI Programming Unleashed
 * CGI Tutorial
 * Using Perl for Web Programming
 * Programming the Perl DBI
 * Database Programming with Perl
 * A Short Guide to DBI
 * Perl & XML
 * Perl & LWP
 * Mastering Perl/Tk
 * Using advanced widgets in Perl/Tk
 * Bioperl course Pasteur Institute
 * Perl for Bioinformatics and Internet Weizmann Institute of Science
 * O'Reilly's CD bookshelf
 * PERL CD bookshelf
 * Approaches to Web Development for Bioinformatics
 * Bioinformatics, Biocomputing and Perl: Instructor's Materials
 * Perl Regular Expressions (With Snippets)
 * Regular expressions in Perl
 * Regular Expressions
 * Perl Regular Expression Mastery
 * Using Regular Expressions
 * Introduction To Regular Expressions
 * A Tao of Regular Expressions
 * Excellent PERL Tutorial@Erack Network
 * Perl 5.8.8 documentation
 * Hash Crash Course
 * How Hashes Really Work
 * Lesk: Introduction to Bioinformatics: 2e
 * Installing and Configuring PHP,MySQL,Perl/CGI and Apache Server
 * Perl and other Book Links

R and BioConductor

 * The R Project for Statistical Computing
 * Bioconductor
 * Books related to R
 * R & BioConductor Manual
 * R Programing
 * A Handbook of Statistical Analyses Using R
 * Statistical Computing with R: A tutorial
 * R Tutorial Basics
 * Statistics with R
 * Using R
 * Using R for psychological research:A simple guide to an elegant package
 * R tutorials with an astronomical dataset
 * NCEAS R Programming Language Resource Center
 * NCEAS R Programming Language Special Topics
 * R Plugins
 * OLIN OSLIN Normalizations
 * Peter's R Programming Pages
 * Visualization Plug-ins for R
 * Heatplus, maCorrPlot, and OCplus

SAS

 * SAS Online Samples
 * Browse SAS Samples
 * Samples from SAS Developers
 * Data Analysis Books for SAS Users
 * UCLA Stat Computing with SAS
 * SAS Online Tutorial

Java & BioJava

 * Sun Java The Java Tutorials
 * Java PLEAC - Programming Language Examples Alike Cookbook PLEAC

Eclipse

 * Eclipse - an open development platform
 * Eclipse Plugin Central (EPIC)
 * Subclipse
 * Bioclipse Home
 * Getting Started with Eclipse 3.1
 * Installing the Eclipse Plugin
 * SWT Programming with Eclipse
 * SWT: The Standard Widget Toolkit
 * Eclpise Books
 * SWT JFace Eclipse Samples
 * Rich Client Platform
 * Eclipse-Plugins.info
 * Eclipse Platform and Plugin Resources
 * Notes on the Eclipse Plug-in Architecture
 * Setting up Eclipse
 * Eclipse Modeling Framework Project (EMF)
 * New Examples of RCP Based Applications

=Microarry Data Analysis=


 * Microarray Expression Data Analysis References
 * A global evaluation of microarray data warehouses ADN
 * My Microarray Software Comparison
 * THE ANALYSIS OF GENE EXPRESSION DATA: METHODS AND SOFTWARE
 * Stanford MicroArray Database
 * Vanderbilt Microarray Shared Resource
 * Bibliography  on Microarray Data Analysis
 * An (Opinionated) Guide to Microarray Data Analysis
 * My Microarray Software Comparison - R packages for microarray analysis
 * FDA Genomic Tool: ArrayTrack
 * Steps in a Typical Data Analysis
 * Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
 * SNOMAD - Standardization and NOrmalization of MicroArray Data
 * PLEXdb Tools-Microarray
 * Microarray Data Mining with Visual Programming
 * GOULPHAR
 * Microarray Core Facility
 * Analysis of Affymetrix Microarray Data --James Wettenhall
 * Microarray Basics PPTs
 * Overview of Lowess Normalization
 * CARMAweb: comprehensive R- and Bioconductor-based web service for microarray data analysis
 * Cluster and TreeView
 * BRB ArrayTools
 * Microarray tools from TIGR
 * NCBI Gene  Expression   Omnibus(GEO)
 * Good Microarrays PPTs

=Algorithms, Data Mining and Data Visualization=


 * Orange Component based data mining software with Visual Programming
 * DAVE Data Analysis and Visualization Environment
 * Ploticus Data visualization
 * KDnuggets Data Mining, Web Mining, Text Mining, and Knowledge Discovery Portal
 * Data Mining and Discovery Machine Learning
 * CLUTO - Family of Data Clustering Software Tools
 * AI, Data Mining, Bioinformatics Websites
 * Cluster 3.0 Open Source Clustering Software
 * WOG: Machine Learning for Data Mining and its Applications
 * Hierarchical Clustering Explorer 3.0
 * HeatMap Builder
 * Data Mining in Bioinformatics
 * Knowledge Discovery In Databases: Tools and Techniques
 * Proteomics and Computation
 * EXACT STRING MATCHING ALGORITHMS
 * Data Mining: Concepts, Algorithms, and Applications *****

=Chemoinformatics or Chemical Informatics=


 * Vorlesung Einführung in die Cheminformatik *****
 * Visual dataflow programming
 * The SDF Toolkit in Perl 5
 * MayaChemTools
 * Pre ADMET Molecular Descriptors Calculation Module
 * Modeling Biomolecular Systems
 * Protégé ontology
 * Chembiogrid.org  Chemical Information Course
 * Algorithm Dictionary
 * World Wide Molecular Matrix web services
 * Protein-Small Ligand Interactions
 * Hacking PubChem with Ruby
 * ChemRuby
 * Mining Patents using Molecular Similarity Search
 * Molsoft
 * Chemistry Software Lists      Linux4Chemistry  NetSci  Chemistry, Biology & Related
 * Chemical Database Systems Basic
 * TORVS Home page of Prof. Gasteiger's research team Presentations  Neural Networks in Chemistry and Drug Design
 * NAR Database Categories List
 * Search ChemExper Chemical Directory
 * Mesa Analytics
 * chemoinf.com
 * CHEMINFORMATICS.ORG
 * Computational Science and Engineering Online (CSE-Online)
 * Daylight Toolkit Programmer's Guide  Meeting Archives   Contrib Changes
 * Fast Calculation of Molecular Polar Surface Area Directly from SMILES
 * BioRPMS - Bioinformatics RPMs Repository

=Math Bio & Complex System Biology=


 * Ordinary Differential Equations using MATLAB *****
 * Nonlinear Dynamics & Chaos Lecture Notes *****
 * Paul's Online Math Notes
 * Solving Differential Equations wit Maple *****
 * Introduction to Differential Equations and Applications (Integration,Linear system of ODE) *****
 * Mathematical Foundations of Systems Biology
 * Mathematics as Biology's New Microscope
 * Dynamical Models in Biology & Differential Equations in Biology
 * Introduction to Control Systems Theory
 * Elementary Differential Equations
 * Discrete and Probabilistic Models in Biology
 * Math in Physiology and Medicine
 * Computational Mathematics
 * Neural Networks & Pattern Recognition
 * Signal Processing
 * Advanced Probability Theory
 * Nonlinear dynamics: How science comprehends chaos Complexity
 * CellML MathML
 * Center for the Study of Complex Systems
 * Complex Systems and Self-Organization
 * Biologically-Inspired Computation
 * COMPLEXITY & CREATIVE INDUSTRIES
 * Topics in Nonlinear Dynamics
 * Nonlinear Dynamics and Chaos
 * Petri Nets World
 * Nonlinear Physics: Modeling Chaos & Complexity
 * Chaos & CompleXity Pdf Library *****
 * Nonlinear dynamics and chaos
 * Interdisciplinary Nonlinear Dynamics
 * Introduction to Computational Science
 * Methods for Ordinary Differential Equations: Nonlinear Dynamics and Chaos
 * A Mathematical Theory of Communication by Claude E. Shannon
 * Information Theory, Inference, and Learning Algorithms
 * Generalized Information Measures and Their Applications
 * Information theory wikipedia
 * Information Theory Primer

=System Biology=
 * Computational Systems Biology and Stochastic π-calculus for Biology
 * Artificial Biochemistry
 * Systems biology Wikipedia
 * European Systems Biology
 * Systems Biology
 * Petri Nets World
 * Petri Nets Tools Database
 * Important Petri Nets Papers

=Ontologies,Semantics Web,Data Integration and Grids=
 * OBO Foundry Ontologies
 * Bio-Ontologies: A List
 * Ontology-driven knowledge system
 * Ontology Development Tools Protégé
 * Biomedical ontologies
 * BioinfoGRID: Bioinformatics Grid Application for life science
 * Data Integration in the Life Sciences





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