tag:blogger.com,1999:blog-36830884026368813112011-12-24T01:40:29.681+08:00Life Science Informatics Resource HubAsif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.comBlogger301100tag:blogger.com,1999:blog-3683088402636881311.post-85393919680345086872042-12-30T21:02:00.000+08:002009-12-23T23:56:05.460+08:00

Life Science Informatics is a marriage between computer sciences and life sciences. This web page serves as a one-stop hub for Life Science Informatics related resources that I use for my research or teaching related activities.

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com2tag:blogger.com,1999:blog-3683088402636881311.post-6113902449437224152011-10-04T21:12:00.002+08:002011-10-04T21:13:28.580+08:00

How great leaders inspire action by Simon Sinek How to live before you die by Steve Jobs The best stats you've ever seen by Hans Rosling Battling bad science by Ben Goldacre The magic of truth and lies on iPods by Marco Tempest How algorithms shape our world by Kevin Slavin Arthur Benjamin does mathemagic Let's use video to reinvent education

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The Daily News@GenomeWebThe Daily Scan@GenomeWebScience DailyWired NewsNature NewsScience NewsScientific AmericaneBioNewsGeneRefSlashdot

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com1tag:blogger.com,1999:blog-3683088402636881311.post-64526310044102590582007-12-29T22:52:00.019+08:002011-10-19T13:40:42.197+08:00

SWAN: Scientific Writing Assistant The Known Universe, A Digital Atlas Pranav Mistry: The thrilling potential of 'SixthSense' technology Fascinating article on Optogenetics - Algae and Light Help Injured Mice Walk Again (mirror link) Adopt a Microbe On Becoming A Scientist The importance of stupidity in scientific research A new way of finding out how diet affects gut microbes Brief Overview

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How To Use Artemis?How To Remove Duplicate Sequences?How To Write A Resume? Get Free Resume TemplatesHow To Run BioSlax On Windows Using VMPlayer?How To Easily Find A Common Meeting Time With Other People?How To Create Firefox Extensions?How To Organize Your Thesis?How To Write A PhD Thesis?How to Write a HypothesesPresentation, Powerpoint And Keynote TipsPresentation Tips By Garr ReynoldsHow Do

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Video tutorials on how to use RAll Kinds Of Biology Related Videos - Highly RecommendedJove - Journal of Visualized ExperimentsInner Life Of A Cell - CoolVideo!5 Minute University - Courtesy of Father Guido SarducciThe PCR SongHow to use BioSlax Live CD@YouTubeELISpot MovieDNA OrigamiThe Common Craft Show - Technology in Plain English

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PSB 2011 - 15th Pacific Symposium On Biocomputing: January 4 - 8; Hawaii, USAAPBC 2011 - 9th Asia Pacific Bioinformatics Conference: January 11 - 14; Incheon, KoreaRECOMB 2011 - 15th Int. Conf. On Research In Molecular Biology: March 28 - 31; Vancouver, CanadaISMB 2011 - 19th Int. Conf. On Intelligent Systems for Molecular Biology: July 15 - 19; ViennaPRIB 2011 - 6th International Conference on

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Bioinformatics, Databases and Software for Medicine Life Science Informatics@Wikia Life Science Informatics Discussion Group@Nature Network PhD Students Discussion Group BiomedExperts - Scientific Social Networking SciLink - An Online Community of Scientists LabRoots -  A Social Networking Site for the Scientific Community

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-3683088402636881311.post-4499168108439268662007-12-26T23:11:00.000+08:002009-12-23T22:49:04.217+08:00

Worldwide Bioinformatics Job Position OffersWorldwide Academia Job Position OffersResources for Graduate Students and Post-Docs: A compilationGraduate Student Resources On The WebMaking the Right Moves: A Practical Guide to Scientific Management for Postdocs and New Faculty, Second EditionRichard Hamming: you and your research

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Search inside College and University websites Across The World (Singapore Will Be Added Soon)S*Star.org Alliance Bioinformatics EducationBioSingapore - Bioinformatics Activities In Singapore

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Khan Academy - A not-for-profit organization with the mission of providing a high quality education to anyone, anywhere. Over 1200+ videos on YouTube covering everything from basic arithmetic and algebra to differential equations, physics, chemistry, biology and finance.iTunes U - Free educational content in students’ handsAcademic Earth - Free online video courses from leading

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-3683088402636881311.post-41088629139022625042007-12-26T23:08:00.000+08:002009-12-23T22:57:13.001+08:00

Life Science Informatics Book Store

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-3683088402636881311.post-31771192762265611402007-12-25T00:19:00.010+08:002011-09-27T15:37:11.634+08:00

BioQuest - Excel Simulations and Tools for Exploratory, Experiential Mathematics Microsoft Biology Tools - Collection of tools that take advantage of the capabilities of the Microsoft Biology Foundation Bioinformatics Links Directory - Curated Links To Molecular Resources, Tools And Databases BioSingapore - Links To Bioinformatics Resources In Singapore Specialized Databases@BIC Computing

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FaBox - an online fasta sequence toolbox PPI-Pred - Protein Protein Interface Prediction FRpred - Collection of methods for the prediction of functional residues in protein multiple sequence alignments PROCHECK - Checks the stereochemical quality of a protein structure Quick2D - Gives an overview of secondary structure of a protein or alignment Ali2D - Plots secondary structure and transmembrane

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NCBIGene@NCBIOMIM@NCBIPubMed@NCBIHubMedRefSeq@NCBITaxonomyBrowser@NCBIKEGG PathwaysPathwayCommonsReactome - open-source, open access, manually curated and peer-reviewed pathway databaseBioCarta - Charting Pathways of LifeiHOP - Information Hyperlinked Over ProteinsPDBUniProtIEDB - Immune Epitope DatabasePfamPrositeGoogle ScholarUCSC Genome BrowserEnsemblJames Watson Genome WebpageJ. Craig Venter

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ProfileGrid -  A new visual representation of large multiple sequence alignments Galaxy - A platform for large-scale, semi-automated, interactive analyses Jalview - Java Alignment Editor Artemis v9 - Free Genome Viewer And Annotation Tool (when saving the file, save as ".jar" instead of ".zip") BioEdit v7.0.9 - Free Sequence Alignment Editor ClustalX 2.0.9 - Free Multiple Sequence Alignment

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com1tag:blogger.com,1999:blog-3683088402636881311.post-7294116638751719282007-12-21T01:28:00.020+08:002011-05-29T12:12:32.725+08:00

Mobyle - An integrated portal for diverse type of sophisticated bioinformatics analyses (highly recommended) PEMer - Construct and analyze structural variants BLASTZ - Multiple sequence alignment program for the whole-genome human-mouse alignments Polyphen - Prediction of Functional Effect of Human nsSNPs SIFT - Sorting Intolerant from Tolerant SNP3D - Assigns Molecular Functional Effects of

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Clustal X - Multiple alignment of nucleic acid and protein sequencesFraise - Powerful lightweight text editorUtopia - A collection of interactive tools for analysing protein sequence and structureCINEMA - Colour INteractive Editor for Multiple AlignmentsAmbrosia - Molecular Structure VieweriRNAi - Dealing with RNAiTargetScanner - Predict microRNA target genesPapers - Your personal library of

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com1tag:blogger.com,1999:blog-3683088402636881311.post-24399443262065455912007-12-20T00:42:00.015+08:002011-01-21T10:34:12.271+08:00

Weka - A collection of machine learning algorithms for data mining tasksHMM: JaneliaSVM: LibSVMANN: Neurodotnet FloodELM: Huang ELM

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-3683088402636881311.post-62804184076785960122007-12-20T00:42:00.014+08:002010-04-04T12:55:07.903+08:00

For details on most of the Apps listed below, click hereChemMobi (free)Promega (free)caBio (free)PubMed On Tap ($2.99) and PubMed on Tap Lite (free)iCut DNA ($4.99)Molecules (free)BioGene (free)GeneIndexAF ($0.99) and GeneIndex (free)Health Sync ($2.99)iProto Human ($4.99)Clinical Trials ($7.99)ChemJuice ($2.99)Illumina's MyGenome (coming soon)My Family Health Portrait (free)iKinase (free)Orkov (

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-3683088402636881311.post-31450107201587534312007-11-20T00:41:00.000+08:002010-01-06T15:42:37.041+08:00

ARB - MHC Binding PredictionHotspot Hunter - T-cell Epitope Hotspot Prediction And AnalysisMicrosoft MHC-I Peptide Energy Binding PredictorMULTIPRED - Promiscuous T-cell Epitopes Prediction (3 HLA Supertypes)NetCTL1.1b@BIC - Promiscous T-cell Epitope Prediction (12 HLA Supertypes)NetCTL1.2@CBS - Promiscous T-cell Epitope Prediction (12 HLA Supertypes)Peptide Binding To MHC Class I Alleles

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Commercial: Schrodinger - Maestro- can get 15 days trial for all modules Discovery studio - can get 1 to 2 months trial MOE (Molecular Operating Environment) SYBYL FLEX-X - can get trial version GOLD ICM DOCKING - can get trial version Non-commercial (free): Autodock vina /version4.0 DOCK6 PATCHDOCK - Online docking server Argus lab CLUSPRO - Protein protein docking ZDOCK - Fast Fourier

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-3683088402636881311.post-28961508810279398752007-09-20T00:42:00.000+08:002010-01-06T15:58:00.148+08:00

GeneralSeqMotifs - A Suite of Web-based Programs to Search for Regulatory Motifs in Prokaryotes and EukaryotesResource on Gene expression regulatory sites and transcription factorsDBD - Taxonomically broad transcription factor predictions: new content and functionalityProkaryotesBioProspector - Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed GenesPRODORIC - Virtual

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ReferencesPMID: 19494180PMID: 18087260 PMID: 12209144 ResourcesFirstEF, Core Promoter, CpG Promoter, Polyadq and JTEFEponineNeural network promoter predictionTranscription element search systemSignal Scan

Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-3683088402636881311.post-38458970133330505942007-07-20T00:41:00.001+08:002010-01-17T14:44:19.696+08:00

ReferencesPMID: 19494180PMID: 18087260 PMID: 12209144 Comparative GenomicsDoublescanSLAMTwinscanHomology Searching CapabilitiesGeneMachineGenscanGenomeScanFgenesh, Fgenes-M,TSSW,TSSG,Polyah, SPL andRNASPLFgenesh, Fgenes-M, SPL and RNASPLHMMgeneGenieGRAILGeneMarkGeneIDGeneParserMZEF and POMBEAAT,MZEF with homologyMZEF with SpliceProximalCheckGenesplicer,Glimmer and

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ReferencesPMID: 19494180PMID: 18087260 PMID: 12209144 ResourcesDioGenesOrfFinderYeastGeneCDS: search coding regionsNeural network splice site predictionNetGene2

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WizFolio Web 2.0 - Free, easy to use with lots of excellent features (highly recommended)Mendeley - Free with lots of excellent featuresEndNote - Good One, But Not FreeZotero - FreeCiteULikeUnique Author IDUnique Paper ID

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Impact Factor 2009 for bioinformatics relevant journals with year by year comparisonH-index compute manually compute automaticallyQuadSearchWeb Of ScienceScopus - Large abstract and citation database of research literature and select web sources

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Cygwin - A Linux-like environment for WindowsAPBioKnoppixBioSLAX Official WebsiteBasic Guide To BioSlax LiveCDHow to Run BioSlax Live CD On You Computer?@YouTubeHow To Run BioSlax VMPlayer version On Your Computer?BioSlax Version Customized For VMPlayerVMPlayer

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Scribd - You Tube for writers; largest social publishing platform (upload as many documents of 100MB or less)Dropbox - Easiest Way to Store, Sync, and, Share Files Online (highly recommended)MediaFire - Free File Hosting Made Simple (free, unlimited data storage, but each of max 200Mb)TeamViewer - All-In-One Solution for Remote Access and Support over the InternetMIkogo - Free screen sharing for

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