Life Science Informatics Resource Hub

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.

Favourite TED videos

• 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

News

• The Daily News@GenomeWeb
  
• The Daily Scan@GenomeWeb
  
• Science Daily
• Wired News
  
• Nature News
• Science News
• Scientific American
  
• eBioNews
• GeneRef
• Slashdot
  

Articles/Sites Of Interest

• 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 of Bioinformatics Activities in Singapore
• Do you know how your brain perceives? Classical, centuries-long beliefs about how our brains work overturned by new understandings
• How to succeed in science: a concise guide for young biomedical scientists. Part I: taking the plunge
• How to succeed in science: a concise guide for young biomedical scientists. Part II: making discoveries
• Chicken Chicken Chicken: Chicken Chicken (this paper actually got published!!)
• The Genographic Project - A Landmark Study Of The Human Journey
• We Move In Mysterious Ways
• Men, Women, And Ghosts In Science
• The Impact Factor Game
• Ten Simple Rules For Doing Your Best Research, According to Hamming
• Ten Simple Rules for Organizing a Scientific Meeting
• Ten Simple Rules For A Good Poster Presentation
• Ten simple rules For making good oral presentations
• Ten Simple Rules For Getting Published
• Ten Simple Rules For Reviewers
• Ten Simple Rules For Selecting A Postdoctoral Position
• Ten Simple Rules For Getting Grants
• Ten Simple Rules For A Successful Collaboration
• Thirty Ways To Improve The Health Of The World's Poorest People
• Economic Inequality Predicts Biodiversity Loss
• PLoS ONE Sandbox: A Place To Learn and Play

Tutorials

• How To Use Artemis?
• How To Remove Duplicate Sequences?
• How To Write A Resume? Get Free Resume Templates
• How 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 Hypotheses
• Presentation, Powerpoint And Keynote Tips
• Presentation Tips By Garr Reynolds
• How Do I Write A Scientific Paper?
• Guidelines For Writing An Effective Scientific Paper
• How To Use NUS Library Proxy Extension?
• How To Memorize Single Letter Amino Acid Code?
• AminoAcidStructure
• Cartoon version of amino acids structure - easy to remember
• Primer on amino acids
• How To Automate BLAST Search?
• How To Edit Wiki Pages?
• How To Upload To Wiki Pages?
• Wiki Cheatsheet
• How To Generate High Quality Publication Figures?
• Visualization in Biology
• Immune Assays In Brief
• Phylogeny For The Faint Of Heart
• How To Create Firefox Extensions?
• What is the difference between alignment position and sequence specific position?

Videos

• Publishing Your Research 101
• Video tutorials on how to use R
• All Kinds Of Biology Related Videos - Highly Recommended
• Jove - Journal of Visualized Experiments
• Inner Life Of A Cell - CoolVideo!
• 5 Minute University - Courtesy of Father Guido Sarducci
• The PCR Song
• How to use BioSlax Live CD@YouTube
• ELISpot Movie
• DNA Origami
• The Common Craft Show - Technology in Plain English

Conferences

• PSB 2011 - 15th Pacific Symposium On Biocomputing: January 4 - 8; Hawaii, USA
  
• APBC 2011 - 9th Asia Pacific Bioinformatics Conference: January 11 - 14; Incheon, Korea
• RECOMB 2011 - 15th Int. Conf. On Research In Molecular Biology: March 28 - 31; Vancouver, Canada
• ISMB 2011 - 19th Int. Conf. On Intelligent Systems for Molecular Biology: July 15 - 19; Vienna
• PRIB 2011 - 6th International Conference on Pattern Recognition in Bioinformatics: September 2 - 4; Delft, the Netherlands
• InCoB 2011 - 10th International Conference On Bioinformatics: November 29 - December 3; Kuala Lumpur, Malaysia
• ECCB 2011 - 10th European Conference On Computational Biology: July 15 - 19; Vienna
• GIW 2011 - 22nd International Conference On Genome Information
• All other bioinformatics conferences
  

Discussion Groups/Networks

• 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

Jobs/Scientific Career Guide

• Worldwide Bioinformatics Job Position Offers
  
• Worldwide Academia Job Position Offers
  
• Resources for Graduate Students and Post-Docs: A compilation
• Graduate Student Resources On The Web
• Making the Right Moves: A Practical Guide to Scientific Management for Postdocs and New Faculty, Second Edition
• Richard Hamming: you and your research
  

Education

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

Short Courses

• 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’ hands
• Academic Earth - Free online video courses from leading universities.
• NCBI Toolkit Course
• EMBO Practical course - computational biology: from genomes to cells and systems
• R workshop
• Linux for beginners
• Scripting Languages - short and quick ways to learn popular scripting languages. Assignments also included to test yourself
• Unix/Shell
• C++
• Perl
• Sed
• BASH Shell
• MySQL
• Ajax
• Coursera: Take the World's Best Courses, Online, For Free.
• Udacity - 21st Century University
• Rosalind - Learn bioinformatics through problem solving
• Venture Lab - Learn, Collaborate, and Create!
• Iversity - Education. Online. Free.

Books

• Life Science Informatics Book Store

Integrated Bioinformatics Database & Analysis Resources/Search Engines

• 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 Resources@BIC
• ExPASy - Proteomics Server
• My NCBI - Helps Customise NCBI Web Services
• VADLO
• Free Online Sequence Analysis Tools@Synamatix
• UGENE - Integrated Bioinformatics Tools
• BioEdit - Biological Sequence Alignment Editor & Other Integrated Analysis Functions
  
• WEMBOSS@BIC, Singapore (see Bioinformatics Web Servers Section for other mirrors)
• DAVID - The Database for Annotation, Visualization and Integrated Discovery
• BioProfiling.de - Analytical Web portal for High-throughput biology

Bioinformatics Web Servers

• 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 regions on an alignment
• CD-Search - Search for Conserved Domains
• MEME - Multiple EM for Motif Elicitation
• Mobyle - An integrated portal for diverse type of sophisticated bioinformatics analyses (highly recommended)
  
• RevTrans - Multiple Alignment Of Coding DNA From Aligned Amino Acid Sequences
• GoPubmed - Search Pubmed And Get Results Sorted Out "GO" and "MESH"
• Blast@BIC
• Blast@NCBI
• ClustalW@BIC
• ClustalW@EBI
• Promals - PROfile Multiple Alignment with Local Structure
• Promals3D - Profile multiple alignment using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints (better than Promals)
  
• CysView - Disulfide Connectivity Analyzer
• WEMBOSS@BIC, Singapore
  
• WEMBOSS@SBRC, Singapore
  
• WEMBOSS@University of Pretoria, South Africa
  
• WEMBOSS@Washington State University, USA
  
• WEMBOSS@Weizmann Institute Server, Israel
  
• WEMBOSS@St. Louis University Server, USA
  
• WEMBOSS@Toulouse Bioinformatics Server, France
  
• WEMBOSS@Wageningen University Server, Netherland
  
• JEMBOSS@BIC, Singapore
  
• Entrez Tools to Retrieve Data from NCBI
• NCBI Tools For Bioinformatics Research
• Swiss-Model - An Automated Comparative Protein Modelling Server
• ModWeb - A Server for Protein Structure Modeling
• ModLoop - Modeling of loops in protein structures
• WHATIF, PROCHECK, VERIFY3D, ERRAT - 3D Model quality check tools
• SUPERPOSE - Quantitative comparison of model with experimental structure
• RExPrimer - is an integrated web-based application for primer design
• Post translation prediction Web-servers/tools 1
• Post translation prediction Web-servers/tools 2 (and other tools)
• Glyco - Glycosylation predictor
• NetNGlyc - N-glycosylation predictor
• EnsembleGly - Glycosylation predictor
• Prosite - Post translation predictor
• Annie - Protein Sequence Annotation and Interpretation Environment
  

Biological Databases

• NCBI
• Gene@NCBI
• OMIM@NCBI
• PubMed@NCBI
• HubMed
• RefSeq@NCBI
• TaxonomyBrowser@NCBI
• KEGG Pathways
• PathwayCommons
• Reactome - open-source, open access, manually curated and peer-reviewed pathway database
• BioCarta - Charting Pathways of Life
  
• iHOP - Information Hyperlinked Over Proteins
  
• PDB
• UniProt
• IEDB - Immune Epitope Database
• Pfam
• Prosite
• Google Scholar
• UCSC Genome Browser
• Ensembl
• James Watson Genome Webpage
• J. Craig Venter Genome Webpage
• InParanoid: Eukaryotic Ortholog Groups
• EggNOG: Evolutionary Genealogy of Genes
• dbSNP - Single Nucleotide Polymorphism
• SRS@EBI
• Mint - Molecular Interaction Database
• Influenza Research Database@BioHealthBase
• Influenza Virus Resource@NCBI
• Japanese Encephalitis Database
  

A Practical Bioinformatician's Basic Toolkit

• 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 Program
• Muscle 3.6 - Free Multiple Sequence Alignment Software
• Promals - PROfile Multiple Alignment with Local Structure
• RASCAL - rapid scanning and correction of multiple sequence alignments
  
• ICM Molsoft v3.6 - Free 3D Molecular Graphics Software
• PyMol - Free Molecular Visualization System
• Rastop - Molecular Visualization Software
  
• Rasmol v2.7.3.1 - Free Molecular Visualization Software
• Modeller - Free 3D Modelling Software
• Beast - Free, cross-platform program for Bayesian MCMC analysis of molecular sequence phylogenetics (cool and powerful!)
  
• MEGA 4 - Free Molecular Evolutionary Genetics Analysis Software
• Phylip 3.68 - Free Phylogeny Inference Package
• TreeView - Free Phylogenetic Tree Drawing Software
• LAPIS - Free, Powerful And Easy To Use Text Manipulation Tool
• Jdotter - Java Dot Plot Alignments
  
• Dotter - A graphical dotplot program Tutorial 1 Tutorial 2
  

A Practical Bioinformatician's Advance Toolkit

• 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 Non-Synonymous SNPs Based on Structure and Sequence Analysis
• PLINK - a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
• PANTHER - Classifies Genes by Their Functions
• iTOL - Interactive Tree of Life
• iPATH - Interactive Pathways Explorer
  
• VisANT - Integrative Visual Analysis Tool for Biological Networks and Pathways
• STITCH - Interaction of networks of chemicals and proteins
• STRING - Proteins and their interactions
• Ka/Ks Calculation tool
• Sirius - An Extensible Molecular Graphics and Analysis Environment
• Local Blast Client - Run blast locally on your computer and on your custom defined dataset
  
• CD-HI/CD-HIT - Clustering tool to identify representative sequences
  
• R Bioconductor - A language and environment for statistical computing and graphics
• R Bioconductor with user-friendly point & click menu
• Gene Pattern - A powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks
• Pebl - Python Environment For Bayesian Learning
• Cytoscape - For visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
• Graphviz - Representing structural information as diagrams of abstract graphs and networks
• Weka - A collection of machine learning algorithms for data mining tasks
• HMMEditor - A visual editor for profile Hidden Markov Model (pHMM)
  

Bioinformatics tools for Mac OS

• Clustal X - Multiple alignment of nucleic acid and protein sequences
• Fraise - Powerful lightweight text editor
• Utopia - A collection of interactive tools for analysing protein sequence and structure
• CINEMA - Colour INteractive Editor for Multiple Alignments
• Ambrosia - Molecular Structure Viewer
• iRNAi - Dealing with RNAi
• TargetScanner - Predict microRNA target genes
• Papers - Your personal library of research
• PubSearch - Fast, efficient PubMed® searching on your Mac and your iPhone / iPod Touch
• EnzymeX - to cur or not to cut; DNA editing
• 4Peaks - For viewing and editing sequence trace files
• R Bioconductor - A language and environment for statistical computing and graphics
• UGENE - Integrated Bioinformatics Tools
• Gene Pattern - A powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks
• HMMEditor - A visual editor for profile Hidden Markov Model (pHMM)
• Weka - A collection of machine learning algorithms for data mining tasks
• Graphviz - Representing structural information as diagrams of abstract graphs and networks
• Cytoscape - For visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
• Plot - A scientific 2D plotting program.
• eBioX - provides an easy-to-use user interface for the eBioTools package
• eBioTools - a collection of more than 300 bioinformatics tools/programs, including
  

1. Boost v1.3.41
2. Clustal W v1.83.UNIX
3. PHYLIP v3.6b
   
4. EMBOSS v5.0.0
   
5. EMBOSS.kaptain v0.98
   
6. gd v2.0.35
   
7. Glimmer v3.02
   
8. HMMER v2.3.2
   
9. INFERNAL v0.7
   
10. Jmol v11.2.12
    
11. Kalign v2
    
12. Kaptain v0.72
    
13. MrBayes v3.1.2
    
14. MRS cust vr482
    
15. MUSCLE v3.6
    
16. NCBI Tools v2.2.16
    
17. NEdit v5.5
    
18. Primer3 v1.1.2
    
19. sim4 v2003-09-21
    
20. soap4r v1.5.8
    
21. Staden v1.7.0
    
22. T-COFFEE v5.05
    
23. ViennaRNA v1.6.5
    

Machine Learning Tools/Methods

• Weka - A collection of machine learning algorithms for data mining tasks
• HMM: Janelia
• SVM: LibSVM
  
• ANN: Neurodotnet Flood
  
• ELM: Huang ELM
  

Life Science Informatics Tools for iPhone

For details on most of the Apps listed below, click here

• ChemMobi (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 (free)

Immunoinformatics Web Servers

• ARB - MHC Binding Prediction
• Hotspot Hunter - T-cell Epitope Hotspot Prediction And Analysis
• Microsoft MHC-I Peptide Energy Binding Predictor
• MULTIPRED - 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 Prediction
• Peptide Binding To MHC Class II Alleles Prediction
• Allele Frequencies
• MHC Motif Viewer
• Epitope Viewer
  

3D Structure Modelling and Docking Suite Software and Tools

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 Transform based protein docking program
• DOT - Macromolecular docking software
• GRAMM-X - Protein-protein docking Web server
• HADDOCK - Data-driven biomolecular docking (protocol)
• Modeller - Free 3D Modelling Software (tutorial)
• SWISS-MODEL - Fully automated protein structure homology-modeling server

Transcription factor binding site prediction tools/software/Web-server

General

• SeqMotifs - A Suite of Web-based Programs to Search for Regulatory Motifs in Prokaryotes and Eukaryotes
  
• Resource on Gene expression regulatory sites and transcription factors
  
• DBD - Taxonomically broad transcription factor predictions: new content and functionality

Prokaryotes

• BioProspector - Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes
  
• PRODORIC - Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes
  
• PRE Detector - Prokaryotic Regulatory Elements Detector
  
• PRODORIC DB - Prokaryotic database of gene regulation
  
• REGULON - Bioinformatics resources for the study of gene regulation in bacteria
  
• FGENESB - Bacterial Operon and Gene Prediction

Eukaryotes

• CompareProspector - Eukaryotic Regulatory Element Conservation Analysis and Identification using Comparative Genomics

Last exon,promoter or TSS prediction

References

• PMID: 19494180
  
• PMID: 18087260
• PMID: 12209144

Resources

• FirstEF, Core Promoter, CpG Promoter, Polyadq and JTEF
  
• Eponine
• Neural network promoter prediction
• Transcription element search system
• Signal Scan
  

Gene Prediction Programs

References

• PMID: 19494180
  
• PMID: 18087260
• PMID: 12209144

Comparative Genomics

• Doublescan
  
• SLAM
  
• Twinscan

Homology Searching Capabilities

• GeneMachine
• Genscan
• GenomeScan
• Fgenesh, Fgenes-M,TSSW,TSSG,Polyah, SPL and
  RNASPL
• Fgenesh, Fgenes-M, SPL and RNASPL
• HMMgene
• Genie
• GRAIL
• GeneMark
• GeneID
• GeneParser
• MZEF and POMBE
• AAT,MZEF with homology
• MZEF with SpliceProximalCheck
• Genesplicer,Glimmer and GlimmerM
• WebGene
• GenLang
• Xpound

Alignment based

• Procrustes
• GeneWise2
• SplicePredictor
• PredictGenes

Ab initio

• Augustus

Finding ORFs and splice sites

References

• PMID: 19494180
  
• PMID: 18087260
• PMID: 12209144

Resources

• DioGenes
• OrfFinder
• YeastGene
• CDS: search coding regions
• Neural network splice site prediction
• NetGene2

Bibliography Reference Manager

• WizFolio Web 2.0 - Free, easy to use with lots of excellent features (highly recommended)
• Mendeley - Free with lots of excellent features
  
• EndNote - Good One, But Not Free
• Zotero - Free
• CiteULike
• Unique Author ID
  
• Unique Paper ID
  

Bibliometrics

• Impact Factor 2009 for bioinformatics relevant journals with year by year comparison
• H-index compute manually compute automatically
• QuadSearch
• Web Of Science
• Scopus - Large abstract and citation database of research literature and select web sources

Free Linux OS For Bioinformaticians

• Cygwin - A Linux-like environment for Windows
• APBioKnoppix
• BioSLAX Official Website
• Basic Guide To BioSlax LiveCD
• How to Run BioSlax Live CD On You Computer?@YouTube
• How To Run BioSlax VMPlayer version On Your Computer?
• BioSlax Version Customized For VMPlayer
• VMPlayer

Miscellaneous Software Downloads/Web Servers

• 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 Internet
• MIkogo - Free screen sharing for people and businesses
• PDF2Word/Excel - Convert PDF documents to MS Word or Excel
  
• Notepad++ - Advanced Text, HTML and Program Editor (free MS Windows Notepad replacement)
  
• Power Edit - Powerful Text, HTML And Program Editor (not free)
  
• EditPlus - Text Editor, HTML Editor And Program Editor (shareware)
  
• Putty - Popular Telnet and SSH Client
• Secure Shell Client - SSH Secure Shell for Windows
  
• WinSCP - Free SFTP, FTP and SCP client for Windows
• CDBurnerXP - Free CD Burner Software
• NUS Library Proxy Extension for Mozilla Firefox (See Tutorial Section For Setup Instructions)
• Bubbl.us - Brainstorm online (mind map)
• Pixlr - Photo editor online
• What Is My IP Address? - Quickly find out your computer's IP address
• Heatmap Builder - Visualization of ‘large number’ experiments like microarray data points representation as boxes of different color shades
• Random.Org - Generating True random number