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.

Essential Bioinformatics Practical Workshop @ FIOCRUZ, Recife, Brazil

• Day 1 Introductory slides
  
• Day1 Practical 0
  
• Day1 Practical 1
• Day1 Practical 1 Solutions
  
• Day1 Practical 2
• Day1 Practical 2 Solutions
• Day2 Practical 3
• Day2 Practical 3 Solutions
  
• Day2 Practical 4
• Day2 Practical 4 Solutions
  
• Local Blast Client
• Day3 Practical 5
• Day3 Practical 5 Solutions
• Day 3 Practical 5 Discussion solutions (slide 7)
  
• Day3 Practical 6
• ModellerWorkingExample
  
• Day3 Practical 6 Solutions

LSM2104, Essential Bioinformatics and Biocomputing @ National University of Singapore

• Tips/Tricks To Improve Productivity
• P2 Discussion Slides
• P2 Discussion Slides Solutions
  
• P3 Discussion Slides
• P3 Discussion Slides Solutions
• P4 Discussion Slides
• P4 Discussion Slides Solutions
  
• P4 Note on wildcard queries
• P5a Discussion Slides
• P5b Discussion Slides
• P6a Discussion part 1
  
• P6a Discussion part 1 Solutions
  
• P6a Discussion part 2
  
• P6a Discussion part 2 Solutions
• P6b Discussion
• P6b Discussion Solutions
• P7 Discussion
  
• P7 Discussion Solutions
  
• P8 Discussion
  
• P8 Discussion Solutions
  
• P9 Discussion
  
• P9 Discussion Solutions
• P10 Discussion Solutions
  
• Miniproject Briefing Round 1
• Miniproject Briefing Round 2
• Miniproject Briefing Round 3
• Miniproject Briefing Round 4
  

Articles/Sites Of Interest

• Impact Factor 2007 for bioinformatics relevant journals with year by year comparison
• Impact Factor for all journals
• 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
• 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?

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

Books

• Life Science Informatics Book Store

Biological Databases

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

• 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

Bioinformatics Web Servers

• 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
• 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 Retreive 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
• 3D Model quality check tools - WHATIF, PROCHECK, VERIFY3D, ERRAT
• Quantitative comparison of model with experimental structure - SUPERPOSE
• 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
  

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
  

A Practical Bioinformatician's Basic Toolkit

• Jalview v2.3
• 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

• 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

Miscellaneous Software Downloads

• NUS Library Proxy Extension for Mozilla Firefox (See Tutorial Section For Setup Instructions)
• Power Edit - Powerful Text, HTML And Program Editor
• EditPlus - Text Editor, HTML Editor And Program Editor
• Putty - Popular Telnet and SSH Client
• WinSCP - Free SFTP, FTP and SCP client for Windows
• CDBurnerXP - Free CD Burner Software

Bibliography Reference Manager

• EndNote - Good One, But Not Free
• Zotero - Open Source And Freely Available
• WizFolio Web 2.0 - Free and allows sharing of literature
  
• CiteULike

Bibliometrics

• Web Of Science
• QuadSearch
• H-index          compute manually          compute automatically
• 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
  

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

• Bioinformatics Jobs Across The World
  

Web-servers / tools to predict transcription factor binding sites

General

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

Prokaryotes

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

Eukaryotes

1. CompareProspector: Eukaryotic Regulatory Element Conservation Analysis and Identification using Comparative Genomics