Abhishek Tiwari:Links

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Contents

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

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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