Abhishek Tiwari:Links: Difference between revisions
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*Signal Processing [http://www.robots.ox.ac.uk/~sjrob/Teaching/b4_sp.html] | *Signal Processing [http://www.robots.ox.ac.uk/~sjrob/Teaching/b4_sp.html] | ||
*Advanced Probability Theory [http://www.robots.ox.ac.uk/~sjrob/Teaching/AdvP/ap.html] | *Advanced Probability Theory [http://www.robots.ox.ac.uk/~sjrob/Teaching/AdvP/ap.html] | ||
*CellML [http://www.cellml.org/] MathML[http://www.w3.org/Math/] | |||
*Center for the Study of Complex Systems [http://www.cscs.umich.edu/~crshalizi/notebooks/] | |||
*Complex Systems and Self-Organization [http://www.cs.utk.edu/~mclennan/Classes/420-594-F03/] | |||
*Biologically-Inspired Computation [http://www.cs.utk.edu/~mclennan/Classes/420/] | |||
*COMPLEXITY & CREATIVE INDUSTRIES [http://www.cci.edu.au/downloads/Jason%20Potts%20Lecture%201.pdf] | |||
*Topics in Nonlinear Dynamics [http://conferenze.dei.polimi.it/siena2003/downloads.html] | |||
Revision as of 08:19, 13 October 2007
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
- Visual dataflow programming [211]
- The SDF Toolkit in Perl 5 [212]
- MayaChemTools [213]
- Pre ADMET Molecular Descriptors Calculation Module [214]
- Modeling Biomolecular Systems [215]
- Protégé ontology [216]
- Chembiogrid.org [217] [218] Chemical Information Course [219]
- Algorithm Dictionary [220]
- World Wide Molecular Matrix web services [221]
- Protein-Small Ligand Interactions [222]
- Hacking PubChem with Ruby [223]
- ChemRuby [224] [225]
- Mining Patents using Molecular Similarity Search [226]
- Molsoft [227]
- Chemistry Software Lists [228] [229] Linux4Chemistry [230] NetSci [231] Chemistry, Biology & Related [232]
- Chemical Database Systems Basic [233]
- TORVS Home page of Prof. Gasteiger's research team [234] Presentations [235] Neural Networks in Chemistry and Drug Design [236]
- NAR Database Categories List [237]
- Search ChemExper Chemical Directory [238]
- Mesa Analytics [239]
- chemoinf.com [240]
- CHEMINFORMATICS.ORG [241]
- Computational Science and Engineering Online (CSE-Online) [242]
- Daylight [243] Toolkit Programmer's Guide [244] Meeting Archives [245] [246] Contrib Changes [247]
- Fast Calculation of Molecular Polar Surface Area Directly from SMILES [248]
- BioRPMS - Bioinformatics RPMs Repository [249]
Math Bio & Complex System Biology
- Mathematical Foundations of Systems Biology [250]
- Mathematics as Biology's New Microscope [251]
- Dynamical Models in Biology & Differential Equations in Biology [252]
- Introduction to Control Systems Theory [253]
- Elementary Differential Equations [254]
- Discrete and Probabilistic Models in Biology [255]
- Math in Physiology and Medicine [256]
- Computational Mathematics [257]
- Neural Networks & Pattern Recognition [258]
- Signal Processing [259]
- Advanced Probability Theory [260]
- CellML [261] MathML[262]
- Center for the Study of Complex Systems [263]
- Complex Systems and Self-Organization [264]
- Biologically-Inspired Computation [265]
- COMPLEXITY & CREATIVE INDUSTRIES [266]
- Topics in Nonlinear Dynamics [267]
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