Abhishek Tiwari:Links

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Programming

Python and Biopython

• Python Programming Language -- Official Website [1]
• BioPython -- Official Website [2]
• Penzilla.net's Python Tutorial [3] [4] MPI on Python [5]*****
• Python course in Bioinformatics Pasteur Institute [6]
• Dave Kuhlman 's WebPage on Python [7]
• Python PLEAC - Programming Language Examples Alike Cookbook [8] PLEAC [9]
• Python Documentation [10]
• An Introduction to Python --Guido van Rossum [11]
• Byte of Python [12]
• Introduction to Python -- Dave Kuhlman [13]
• Advanced Python Topics -- Dave Kuhlman [14]
• Programming for Bioinformatics in Python [15]
• Introduction to Programming using Python for Biologists at the Pasteur Institute [16]
• Python HOWTOs [17] Regular Expression HOWTO [18]
• Python Programming Tutorial Richard G Baldwin [19]
• Beginning Python for Bioinformatics by Patrick O'Brien [20]
• A Beginner's Python Tutorial [21]
• Python Tutorials List and Links [22]
• Python:Choose Your GUI Toolkit [23]
• Building GUI Applications with PythonCard and PyCrust [24]
• Python Library Reference [25]
• Python Tutorial --Guido van Rossum [26]
• Biopython Tutorial and Cookbook --Jeff Chang, Brad Chapman, Iddo Friedberg [27]
• Python for Structural Bioinformatics [28]
• Python: A Programming Language for Software Integration and Development [29]
• Bioinformatics (Programming Python for Bioinformatics) [30]
• Python in Bioinformatics and Chemical Informatics [31]
• Beginning Python for Bioinformatics [32]
• Using Python to solve problems in bioinformatics [33]
• SciPy Scientific Tools for Python [34]
• NumPy N-dimensional Array manipulations [35]
• Topical Software Links categorized by scientific discipline or computational topic [36]
• Open Source Free Python CGI Scripts for Molecular Biology and Bioinformatics [37]
• AstraZeneca Uses Python for Collaborative Drug Discovery [38]
• Dive Into Python [39]
• Other Python links [40]

Perl and BioPerl

• Perl.org [41] use Perl;[42]
• Perl.com [43]
• ActivePerl [44]
• Perl Paraphernalia by Mark Jason Dominus [45] Coping with Scoping [46] Higher-Order Perl [47]
• Perl Circus [48] Regex [49] Hashes [50]
• perlmeme.org [51] HOWTO [52] TUTORIALs [53] index()[54] Regular expressions [55]
• Comprehensive Perl Archive Network [56]
• Perl PLEAC - Programming Language Examples Alike Cookbook [57] PLEAC [58]
• BioPerl [59]
• Perl in a Nutshell [60] [61]
• Learning Perl [62] [63]
• Learning Perl on Win32 [64]
• Programming Perl [65][66]
• Advanced Perl Programming [67]
• Perl for System Administration [68]
• Perl Cookbook [69]
• The Perl You Need to Know -Aaron Weiss [70] -Stas Bekman [71][72] [73] [74]
• CGI Programming with Perl [75]
• CGI Programming on the World Wide Web [76]
• CGI Programming 101: Learn CGI Today! [77]
• CGI Programming Unleashed [78]
• CGI Tutorial [79]
• Using Perl for Web Programming [80]
• Programming the Perl DBI [81] [82]
• Database Programming with Perl [83] [84]
• A Short Guide to DBI [85]
• Perl & XML [86]
• Perl & LWP [87]
• Mastering Perl/Tk [88] [89]
• Using advanced widgets in Perl/Tk [90]
• Bioperl course Pasteur Institute [91]
• Perl for Bioinformatics and Internet Weizmann Institute of Science [92]
• O'Reilly's CD bookshelf [93]
• PERL CD bookshelf [94]
• Approaches to Web Development for Bioinformatics [95]
• Bioinformatics, Biocomputing and Perl: Instructor's Materials [96]
• Perl Regular Expressions (With Snippets) [97]
• Regular expressions in Perl [98]
• Regular Expressions [99]
• Perl Regular Expression Mastery [100] [101]
• Using Regular Expressions [102]
• Introduction To Regular Expressions [103]
• A Tao of Regular Expressions [104]
• Excellent PERL Tutorial@Erack Network [105]
• Perl 5.8.8 documentation [106]
• Hash Crash Course [107]
• How Hashes Really Work [108]
• Lesk: Introduction to Bioinformatics: 2e [109]
• Installing and Configuring PHP,MySQL,Perl/CGI and Apache Server [110]
• Perl and other Book Links [111] [112] [113] [114]

R and BioConductor

• The R Project for Statistical Computing [115]
• Bioconductor [116]
• Books related to R [117]
• R & BioConductor Manual [118]
• R Programing [119]
• A Handbook of Statistical Analyses Using R [120]
• Statistical Computing with R: A tutorial [121]
• R Tutorial Basics [122]
• Statistics with R [123]
• Using R [124]
• Using R for psychological research:A simple guide to an elegant package [125]
• R tutorials with an astronomical dataset [126] [127]
• NCEAS R Programming Language Resource Center [128]
• NCEAS R Programming Language Special Topics [129]
• R Plugins [130]
• OLIN OSLIN Normalizations [131]
• Peter's R Programming Pages [132] [133]
• Visualization Plug-ins for R [134]
• Heatplus, maCorrPlot, and OCplus [135]

SAS

• SAS Online Samples [136]
• Browse SAS Samples [137]
• Samples from SAS Developers [138]
• Data Analysis Books for SAS Users [139]
• UCLA Stat Computing with SAS [140]
• SAS Online Tutorial [141]

Java & BioJava

• Sun Java [142] The Java Tutorials [143]
• Java PLEAC - Programming Language Examples Alike Cookbook [144] PLEAC [145]

Eclipse

• Eclipse - an open development platform [146]
• Eclipse Plugin Central (EPIC) [147]
• Subclipse [148]
• Bioclipse Home [149]
• Getting Started with Eclipse 3.1 [150]
• Installing the Eclipse Plugin [151]
• SWT Programming with Eclipse [152]
• SWT: The Standard Widget Toolkit [153]
• Eclpise Books [154] [155]
• SWT JFace Eclipse Samples [156]
• Rich Client Platform [157]
• Eclipse-Plugins.info [158]
• Eclipse Platform and Plugin Resources [159]
• Notes on the Eclipse Plug-in Architecture [160]
• Setting up Eclipse [161]
• Eclipse Modeling Framework Project (EMF) [162]
• New Examples of RCP Based Applications [163]

Microarry Data Analysis

• Microarray Expression Data Analysis References [164]
• A global evaluation of microarray data warehouses ADN [165]
• My Microarray Software Comparison [166]
• THE ANALYSIS OF GENE EXPRESSION DATA: METHODS AND SOFTWARE [167]
• Stanford MicroArray Database [168]
• Vanderbilt Microarray Shared Resource [169] [170]
• Bibliography on Microarray Data Analysis [171]
• An (Opinionated) Guide to Microarray Data Analysis [172]
• My Microarray Software Comparison - R packages for microarray analysis [173]
• FDA Genomic Tool: ArrayTrack [174]
• Steps in a Typical Data Analysis [175]
• Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments [176]
• SNOMAD - Standardization and NOrmalization of MicroArray Data [177] [178]
• PLEXdb Tools-Microarray [179]
• Microarray Data Mining with Visual Programming [180]
• GOULPHAR [181]
• Microarray Core Facility [182]
• Analysis of Affymetrix Microarray Data --James Wettenhall [183] [184]
• Microarray Basics PPTs [185]
• Overview of Lowess Normalization [186]
• CARMAweb: comprehensive R- and Bioconductor-based web service for microarray data analysis [187]
• Cluster and TreeView [188]
• BRB ArrayTools [189]
• Microarray tools from TIGR [190]
• NCBI Gene Expression Omnibus(GEO) [191]
• Good Microarrays PPTs [192]

Algorithms, Data Mining and Data Visualization

• Orange Component based data mining software with Visual Programming [193]
• DAVE Data Analysis and Visualization Environment [194]
• Ploticus Data visualization [195]
• KDnuggets Data Mining, Web Mining, Text Mining, and Knowledge Discovery Portal [196] [197]
• Data Mining and Discovery [198] Machine Learning [199]
• CLUTO - Family of Data Clustering Software Tools [200]
• AI, Data Mining, Bioinformatics Websites [201]
• Cluster 3.0 Open Source Clustering Software [202]
• WOG: Machine Learning for Data Mining and its Applications [203]
• Hierarchical Clustering Explorer 3.0 [204]
• HeatMap Builder [205]
• Data Mining in Bioinformatics [206]
• Knowledge Discovery In Databases: Tools and Techniques [207]
• Proteomics and Computation [208]
• EXACT STRING MATCHING ALGORITHMS [209]
• Data Mining: Concepts, Algorithms, and Applications [210]*****

Chemoinformatics or Chemical Informatics

• Vorlesung Einführung in die Cheminformatik [211]*****
• Visual dataflow programming [212]
• The SDF Toolkit in Perl 5 [213]
• MayaChemTools [214]
• Pre ADMET Molecular Descriptors Calculation Module [215]
• Modeling Biomolecular Systems [216]
• Protégé ontology [217]
• Chembiogrid.org [218] [219] Chemical Information Course [220]
• Algorithm Dictionary [221]
• World Wide Molecular Matrix web services [222]
• Protein-Small Ligand Interactions [223]
• Hacking PubChem with Ruby [224]
• ChemRuby [225] [226]
• Mining Patents using Molecular Similarity Search [227]
• Molsoft [228]
• Chemistry Software Lists [229] [230] Linux4Chemistry [231] NetSci [232] Chemistry, Biology & Related [233]
• Chemical Database Systems Basic [234]
• TORVS Home page of Prof. Gasteiger's research team [235] Presentations [236] Neural Networks in Chemistry and Drug Design [237]
• NAR Database Categories List [238]
• Search ChemExper Chemical Directory [239]
• Mesa Analytics [240]
• chemoinf.com [241]
• CHEMINFORMATICS.ORG [242]
• Computational Science and Engineering Online (CSE-Online) [243]
• Daylight [244] Toolkit Programmer's Guide [245] Meeting Archives [246] [247] Contrib Changes [248]
• Fast Calculation of Molecular Polar Surface Area Directly from SMILES [249]
• BioRPMS - Bioinformatics RPMs Repository [250]

Math Bio & Complex System Biology

• Ordinary Differential Equations using MATLAB [251]*****[252]
• Nonlinear Dynamics & Chaos Lecture Notes [253]*****
• Paul's Online Math Notes [254]
• Solving Differential Equations wit Maple [255]*****
• Introduction to Differential Equations and Applications (Integration,Linear system of ODE) [256]*****
• Mathematical Foundations of Systems Biology [257]
• Mathematics as Biology's New Microscope [258]
• Dynamical Models in Biology & Differential Equations in Biology [259]
• Introduction to Control Systems Theory [260]
• Elementary Differential Equations [261]
• Discrete and Probabilistic Models in Biology [262]
• Math in Physiology and Medicine [263]
• Computational Mathematics [264]
• Neural Networks & Pattern Recognition [265]
• Signal Processing [266]
• Advanced Probability Theory [267]
• Nonlinear dynamics: How science comprehends chaos [268] Complexity [269]
• CellML [270] MathML[271]
• Center for the Study of Complex Systems [272]
• Complex Systems and Self-Organization [273]
• Biologically-Inspired Computation [274]
• COMPLEXITY & CREATIVE INDUSTRIES [275]
• Topics in Nonlinear Dynamics [276]
• Nonlinear Dynamics and Chaos [277]
• Petri Nets World [278]
• Nonlinear Physics: Modeling Chaos & Complexity [279] [280]
• Chaos & CompleXity Pdf Library [281]*****
• Nonlinear dynamics and chaos [282]
• Interdisciplinary Nonlinear Dynamics [283]
• Introduction to Computational Science [284]
• Methods for Ordinary Differential Equations: Nonlinear Dynamics and Chaos [285]
• A Mathematical Theory of Communication by Claude E. Shannon [286]
• Information Theory, Inference, and Learning Algorithms [287]
• Generalized Information Measures and Their Applications [288]
• Information theory wikipedia [289]
• Information Theory Primer [290]

System Biology

• Computational Systems Biology and Stochastic π-calculus for Biology [291] [292][293]
• Artificial Biochemistry [294]
• Systems biology Wikipedia [295]
• European Systems Biology [296]
• Systems Biology [297]
• Petri Nets World [298]
• Petri Nets Tools Database [299]
• Important Petri Nets Papers [300][301][302][303][304][305][306][307]

Ontologies,Semantics Web,Data Integration and Grids

• OBO Foundry Ontologies [308]
• Bio-Ontologies: A List [309]
• Ontology-driven knowledge system [310]
• Ontology Development Tools Protégé [311]
• Biomedical ontologies [312]
• BioinfoGRID: Bioinformatics Grid Application for life science [313]
• Data Integration in the Life Sciences [314]

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