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Programming Languages, Conferences, Hot Topics, Academic Programs & Companies

1. Programming
   
   1. Perl
      
      1. Basic procedural scripting language
         
      2. Freely available, runs on any platform
         
      3. Does not need a compiler, just a simple text editor
         
      4. Forms the core of most Bioinformatics applications
         
      5. Relatively easy to learn
         
      6. Courses available
         
         • PERL and CGI: Introduction
      7. Recommended books
         
         • Learning Perl, 2nd Edition By Randal L. Schwartz & Tom Christiansen
         • Programming Perl, 2nd Edition By Larry Wall, Tom Christiansen & Randal L. Schwartz
         • Perl Cookbook By Tom Christiansen & Nathan Torkington
         • Advanced Perl Programming By Sriram Srinivasan
         • Mastering Regular Expressions By Jeffrey E. F. Friedl
         • Mastering Algorithms with Perl By Jon Orwant, Jarkko Hietaniemi & John Macdonald
      8. Recommended websites
         
         • Bio Perl Project
           http://bio.perl.org/
           
           • The primary resource for using Perl in biology
             
           • Archive of scripts, modules etc. Look here before re-writing it yourself
             
           • Great source for help. Very friendly people.
             
           • Maintain an active mailing list
             
         • The Open Lab - http://theopenlab.uml.edu/
           
           • A not-for-profit foundation established to sponsor open collaborations in research and software development in the scientific field of computational biology.
             
         • The Perl Institute
           http://www.perl.org/
           
         • Comprehensive Perl Archive Network (CPAN)
           http://www.cpan.org/
           
   2. Java
      
      1. Object oriented, cross-platform language
         
      2. Freely available
         
      3. Requires a compiler, free compiler available with the JDK
         
      4. Has a bright future in Bioinformatics
         
      5. Relatively easy to get started, can quickly become complex
         
      6. Courses available
         

         Java: Network Programming Techniques

         Java Programming III : Object-Oriented Java Programming

         Java Programming II: Beginning Java Programming

         Java Programming IV : Advanced Java Programming Structures

         Java Programming I : Fundamental Java Concepts

         Graphical User Interface with JFC

         Java Programming

         TCP/IP Internet Architecture and Protocols, Part II

      7. Recommended books
         
         • Java How to Program -3rd Edition by Paul J. Deitel, Harvey M. Deitel
      8. Recommended websites
         
         • JaMBW - Java Molecular Biology Workbench
           http://www.embl-heidelberg.de/JaMBW/main.html
           
   3. C/C++
      1. procedural (C)/object oriented (C++)
      2. Requires compiler, some freely available for example at http://www.gnu.org/
      3. used where speed and direct memory access are important
      4. learning curve fairly steep
      5. Courses available
         

         C/C++ Programming III : Intermediate Programming with Objects

         C/C++ Programming II : Dynamic Memory and File I/O Concepts

         C/C++ Programming I : Fundamental Programming Concepts

         C/C++ Programming IV: Advanced Programming with Objects

         C Programming

         Visual C++ Programming

         C++ Programming

         Embedded Controller Programming II: Embedded C

         C Programming I

      6. Recommended Books
         
         • A Book on C: Programming in C By Al Kelly & Ira Pohl
         • C++ Primer by Stanley B. Lippman, Josee Lajoie & Jose Lajoie
         • The C++ Programming Language By Bjarne Stroustrup
      7. Recommended websites
         
         • An Introduction to C programming
           http://www.cit.ac.nz/smac/cprogram/
   4. SQL
      
      1. Not a "stand-alone" programming language
         
      2. Procedural
         
      3. Very easy to learn initial concepts
         
      4. Essential for working with true databases (Oracle, Sybase, MySQL)
         
      5. Courses available
         
         • SQL Programming
      6. Recommended books
         
         • The Practical Sql Handbook : Using Structured Query Language by Judith S. Bowman, Sandra L. Emerson, Marcy Darnovsky
         • SQL for Dummies By Allan G. Taylor
         • Using SQL; R. Colburn, QUE
2. Hot Topics
   
   1. Arrays and Expression Arrays
      
      1. NHGRI Microarray Project
         http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/
         
      2. Build your own arrayer
         http://cmgm.stanford.edu/pbrown/mguide/index.html
         
      3. Affymetrix
         http://www.affymetrix.com/
         
      4. Other resources
         http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/microlinks.html
         
   2. SAGE - Serial Analysis of Gene Expression
      
      1. Description of SAGE
         http://www.sagenet.org/home/Description.htm
         
         • A short sequence tag (10-14bp) contains sufficient information to uniquely identify a transcript provided that that the tag is obtained from a unique position within each transcript
           
         • Sequence tags can be linked together to from long serial molecules that can be cloned and sequenced
           
         • Quantitation of the number of times a particular tag is observed provides the expression level of the corresponding transcript.
           
      2. Resources
         
         • NCBI
           http://www.ncbi.nlm.nih.gov/SAGE/
           
         • SAGE Net
           http://www.sagenet.org/
           
         • Genzyme Molecular Oncology
           http://www.genzyme.com/prodserv/molecular_oncology/sage/welcome.htm
           
   3. Bioinformatics Portals or ASPs (Application Service Providers)
      Basic idea: More efficient to have a central location to house expensive hardware and software with expert service provider on well maintained machines than to buy yourself.
      Advantages
      User pays for access to software as they use it
      Users have access to more different types of software than they could afford on their own
      ASPs provide a permanent place for storage of data and analysis results
      Disadvantages
      May be hard to maintain competence in house, resulting in risky level of dependance on the ASP
      Slowdowns or failures at the ASP could delay research
      
      1. Fee for Service Model ASPs
         
         • GCG's SeqWeb and Viaken
           http://www.oxmol.com
           http://www.viaken.com
           
           • Uses GCG's SeqStore data management product which is a central database to store sequence data, primers, plasmids, etc
             
           • Secure internet access
             
           • Good technical support from Viaken
             
         • eBioinformatics
           http://www.ebioinformatics.com
           
           • Has it's own suite of web based tools called BioNavigator
             
           • Usage based fees for time used and amount of data stored
             
           • Access to GCG programs through SeqWeb
             
           • Access to proprietary software and databases
             
           • Tools include PCR primer design, restriction mapping, protein secondary structure, database searching, multiple alignments and phylogenetic tree production
             
         • GeneSolutions
           http://www.genesolutions.com
           
           • Pay as you go
             
           • Access to Hyseq's proprietary database of 12 million+ sequences (mostly EST's), many rarely expressed
             
           • Free access to store and run searches, pay to see the results
             
           • Larger fees to get the clones corresponding to a search result
             
           • Many tissue specific expression profiles for 50 tissue libraries, which can be added to the search results for another fee
             
         • LabOnWeb
           http://www.labonweb.com
           
           
           • LabOnWeb elongates your query sequence to a full gene.
             
           • Lists tissues in which your gene is probably expresssed based on SAGE data.
             
           • Extensive sequence analysis includes gene function prediction, mapping and much more.
             
           • Based on data from all major public and on proprietary data
             
           • Two analysis per day free, pay for the rest by credit card
             

           
           

      2. "Free" ASPs
         
         • DoubleTwist
           http://www.doubletwist.com
           
           • Automatic research agents to perform simple bioinformatic operations
             
           • Can store your sequences and results on their site
             
           • Many proprietary software and databases are available
             
           • Many partnerships with vendors such as Alphagene, Invitrogen and Clontech such that you can purchase a clone from them if it was found in your result set
             
         • The Biology Workbench
           http://workbench.sdsc.edu/
           
           • Single web interface to a wide variety of standard protein and nucleic acid analysis programs
             
           • Can store sequences and results on their site
             
           • Password protected and encrypted
             
           • Many database searches available, don't have to worry about format issues
             
         • GeneScape Portal
           http://curatools.curagen.com/
           
           • Store your sequences and results on their site
             
           • Access proprietary CuraTools to perform a wide variety of database searches and analysis for DNA and protein
             
           • Includes BLAST, Clustal W, CAP2, PROSITE, PRODOM, Pfam, etc
             
         • Amplicom
           http://www.amplicom.com/
           
           • A true portal site, with much more than just bioinformatics tools
             
           • Integrates genetic sequence data from 11,000 human genes , 6849 mouse genes, 6,307 yeast and 14,190 C elegans genes, 16 bacteria complete genomes and 5 Archaea complete genomes
             
           • Provides links to a wide variety of analysis tools
             
3. Conferences
   
   1. Cambridge Health Institute Conference Series
      1. Bioinformatics
         
      2. Integrated Bioinformatics
         
      3. In Silico Biology
         
      4. Proteomics
         
      5. Functional Genomics
         
   2. Drug Discovery Technology 2001   Organized by IBC USA Conferences
      August 13-17, 2001,   Boston, MA
   3. GCB2001   16^th German Conference on Bioinformatics
      October 7 - 10, 2001 Braunschweig, Germany
   4. PSB 2002 - Pacific Symposium on Biocomputing
      January 2-8, 2002 Kaua'i Marriott, Kaua'i
   5. RECOMB 2001
      April 21-24, 2001, Montreal, Canada
      
   6. ISMB 2002 - Intelligent Systems for Molecular Biology
      August 3 - 7, 2002 Edmonton, Canada
      
4. Academic Programs
   The primary organization for Bioinformatics is the International Society for Computational Biology (http://www.iscb.org/). They have a large list of courses available.
   
   1. Online
      
      1. Sequence Analysis with Distributed Resources
         http://bibiserv.techfak.uni-bielefeld.de/sadr/
         
      2. Bioinformatics Certificate Program at Stanford University
         http://scpd.stanford.edu/ce/ndp/certificate/bioinformatics.html
         
      3. Universit?t Bielefeld, VSNS Biocomputing Division
         http://merlin.mbcr.bcm.tmc.edu:8001/bcdusa/welcome.html
         
      4. The Principles of Protein Structure using the Internet
         http://www.cryst.bbk.ac.uk/PPS2/index.html
         
      5. Getting the most from your hidden Markov Model
         http://www.cse.ucsc.edu/research/compbio/ismb99.tutorial.html
         
   2. Regular
      
      1. Degree Programs
         
         • Stanford University Bioinformatics Program
           http://www-smi.stanford.edu/people/altman/bioinformatics.html
           
         • University of California-Irvine Biomedical Informatics program
           http://www.ics.uci.edu/~biomed/
           
         • University of California-Santa Cruz Computational Biology Program
           http://www.cse.ucsc.edu/research/compbio/
           
         • University of California-San Francisco Program in Medical Information Sciences
           http://www.mis.ucsf.edu/
           
         • University of Southern California, Center for Computational and Experimental Genomics
           http://hto-e.usc.edu/index.html
           
      2. Courses
         
         • University of California-San Diego, Computational Biology (CSE 290)
           http://www.cs.ucsd.edu/~rik/courses/cse290-w99/index.html
           
         • University of California-Santa Cruz, Bioinformatics (CMP 243)
           http://www.cse.ucsc.edu/classes/cmp243/
           
         • University of California-Santa Cruz, Bioinformatics Research Seminar (CMP 280)
           http://www.cse.ucsc.edu/~karplus/280B/
           
5. Job Finding and General Information
   
   1. Biospace
      http://www.biospace.com
      
   2. BioPlanet
      http://www.bioplanet.com
      
      1. Designed specifically for Bioinformatics
         
   3. GenomeJobs
      http://www.genomejobs.com
      
   4. BioView
      http://www.bioview.com
      
6. Bioinformatics Companies
   
   1. DoubleTwist.com
      http://www.doubletwist.com
      
      1. Type of products
         
         • Thin-client/server software
           
      2. Main products
         
         • GeneMill - project management software designed for DNA sequencing laboratories
           
         • GeneWorld - comprehensive sequence analysis and annotation solution
           
         • EST Clustering tools - allow rapid clustering and alignment of both ESTs and full-length sequences
           
         • Pathway Tools - computationally predict pathways from genomic data
           
   2. Molecular Simulations Inc.
      http://www.msi.com
      
      1. Product type - 3D simulation software
         
      2. Main products
         
         • Cerius2 - Simulation environment for life and materials science
           
         • WebLab - Web browser plug-in that allows molecular simulation and analysis
           
         • Insight II - 3D graphical environment for molecular modeling
           
         • Catalyst - Modeling, hypothesis generation and structure for drug discovery
           
         • FELIX - Processing, display and analysis of NMR data
           
         • QUANTA - Advanced tools for macromolecular X-ray crystallographers
           
   3. MDL Information Systems
      http://www.mdli.com
      
      1. Developer of the CHIME plugin
         
      2. Product type - Software packages
         
      3. Target audience - Drug companies and cheminformatics
         
      4. Too many products to list
         
   4. Incyte
      http://www.incyte.com
      
      1. Product type - Information and software
         
      2. Main products
         
         • LifeSeq database collection - LifeSeq Gold currently contains 4.3 million ESTs, 3.3 million of which are Incyte-proprietary. This represents an estimated 90% of expressed human genes
           
         • PathoSeq database collection - provides genetic data for a variety of microorganisms, with a focus on disease-causing bacteria and fungi.
           
         • LifeTools - scalable, enterprise-wide system for processing, storing, analyzing, and managing both proprietary and public-domain genomic data. It gives scientists extensive project management capabilities, including the ability to track research projects, and easily share data with team members
           
         • Microarrays - A wide variety of Human, plant and animal arrays and the software to analyze them
           
   5. Neomorphic Software
      http://www.neomorphic.com
      
      1. Product type - Java-based bioinformatics tools
         
      2. Main Products
         
         • Genome SDK - an advanced Java class library that can be tailored to a client's in-house bioinformatics requirements. Put the widgets together and coordinate them to provide dynamic displays of your data
           
         • Labtrak - laboratory information management system. Neomorphic will configure Labtrack for your unique laboratory process.