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 frequently use for my research or teaching related activities.

News

• Nature News
• Science News
• Science Daily
• Scientific American
  
• eBioNews
• GeneRef
  

Articles/Sites Of Interest

• Pranav Mistry: The thrilling potential of 'SixthSense' technology
  
• Fascinating article on Optogenetics - Algae and Light Help Injured Mice Walk Again (mirror link)
  
• 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 compute H-index using Web of Science
• 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?
• 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?
• 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

• 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
  

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

LSM2241, Introductory Bioinformatics @ National University of Singapore

• Coming Soon for AY0910 Semester 2
  

Books

• Life Science Informatics Book Store

LSM3241 - Bioinformatics And Biocomputing

• LSM3241Wiki
• BioSlax
• How to use BioSlax Live CD@YouTube
• LAMS Server@NUS BIC
• LAMS Tutorial
  

Integrated Bioinformatics Resources/Search Engines

• 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
  

Biological Databases

• NCBI
• Gene@NCBI
• OMIM@NCBI
• PubMed@NCBI
• HubMed
• RefSeq@NCBI
• TaxonomyBrowser@NCBI
• KEGG Pathways
• PathwayCommons
• 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
  

Bioinformatics Web Servers

• 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
  

A Practical Bioinformatician's Basic Toolkit

• 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
• ICM Molsoft v3.6 - Free 3D Molecular Graphics Software
• PyMol - Free Molecular Visualization System
• Rasmol v2.7.3.1 - Free Molecular Visualization Software
• Modeller 9v3 - Free 3D Modelling Software
• 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
• Dotter 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
• PANTHER - Classifies Genes by Their Functions
• iTOL - Interactive Tree of Life
• iPATH - Interactive Pathways Explorer
  
• 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
• R - a language and environment for statistical computing and graphics
  

Bioinformatics tools for Mac OS

• 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
    

3D Structure Modelling and Docking Suit 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 - for protein protein docking

Miscellaneous Software Downloads

• Dropbox
• TeamViewer
  
• 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
• 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)

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

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
  

Machine Learning

• HMM: Janelia
• SVM: LibSVM
  
• ANN
• ELM

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

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
  

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
  

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 (highly recommended)
  
• EndNote - Good One, But Not Free
• Zotero - Free
• CiteULike

Bibliometrics

• Impact Factor 2008 for bioinformatics relevant journals with year by year comparison
• Impact Factor for all journals
• 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

• 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

Courses

• 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

Conferences

• PSB 2009 - 14th Pacific Symposium On Biocomputing: January 5 - 9; Hawaii
• APBC 2009 - 7th Asia Pacific Bioinformatics Conference: January 13 - 16; Beijing, China
• RECOMB 2009 - 13th Int. Conf. On Research In Molecular Biology: May 18 -21; Tucson, Arizona, USA
• EABN 2008 - 3rd East Asia Bioinformation Network: April 18; Singapore
• 2nd Asean-China International Bioinformatics Workshop 2008: April 17-18; Singapore
• ISMB 2008 - 16th Int. Conf. On Intelligent Systems for Molecular Biology: July 19 - 23; Toronto, Canada
• First Pan-American Dengue Research Network Meeting: July 23-25; Recife, Brazil
• ISCB 2008 - 9th Int. Conf. On Systems Biology: August 22 - 28; Gothenburg, Sweden
• GCB 2008 - German Conference on Bioinformatics 2008: September 9-12; Dresden, Germany
• ECCB 2008 - 7th European Conference On Computational Biology: September 22 - 26; Cagliari, Italy
• PRIB 2008 - Third IAPR International Conference on Pattern Recognition in Bioinformatics: October 15 – 17; Novotel St Kilda, Melbourne , Australia
• JITMM 2008 - Joint International Tropical Medicine Meeting: October 13-14; Bangkok, Thailand
  
• The Second International Conference On Dengue And Dengue Haemorrhagic Fever, 2008: October 15 - 17; Phuket, Thailand
• InCoB 2008 - Seventh International Conference On Bioinformatics: October 20-22; Taiwan
• GIW 2008 - 19th International Conference On Genome Informatics: December 1 - 3; Brisbane, Australia
• Innovations'08 - 5th International Conference On Innovations In Information Technology: December 16-18; Abu Dhabi, UAE

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

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