Approaches to Web Development for Bioinformatics

Medical Computing > Web Development for Bioinformatics > References
Contents

About the Author

Alex Amies is a software engineer.  He has a BS in Computer Science from the University of New South Wales and an MS in Engineering from Stanford University.  He can be contacted at alexamies@gmail.com.

Related Reading

  1. Alex Amies, 2006.  Open Source Software and Documentation for Chemistry and Biomedical Sciences.
  2. Alex Amies, 2006.  Basic Biological Chemistry with Extensible Markup Language.
  3. Alex Amies, 2006.  Getting Started Developing Interactive Web Interfaces for Scientific and Medical Applications.

References

  1. Oak Ridge National Laboratory, The Human Genome Project  web page at www.ornl.gov/sci/techresources/Human_Genome/home.shtml.
  2. National Center for Biotechnology Information (NCBI), GenBank database at www.ncbi.nih.gov/Genbank.  The MapViewer is at www.ncbi.nlm.nih.gov/mapview/.  The NCBI Handbook is at www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.  Gene data can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/gene/.  Human genome information can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/.  The rna.gbk file is at ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.gbk.gz.  The Entrez Utilities page is at http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html.  The Whole Genome Association web site is at http://www.ncbi.nlm.nih.gov/WGA/.  Conserved Domains Database is at www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd.
  3. European Bioinformatics Institute tools and databases page at www.ebi.ac.uk/services/. 
  4. Swiss Institute of Bioinformatics (SIB), ExPASy (Expert Protein Analysis System) at http://www.expasy.ch/.  Basic translation tool is at http://www.expasy.ch/tools/dna.html.
  5. Kyoto Genes and Genome (KEGG) database hosted by the Bioinformatics Center at the Institute of Chemical Research, Kyoto University at http://www.genome.jp/kegg/genes.html.
  6. The Institute for Genomic Research (TIGR) at www.tigr.org.
  7. EMBOSS: The European Molecular Biology Open Software Suite (2000)  Rice, P. Longden, I. and Bleasby, A.  Trends in Genetics 16, (6) pp276--277.  Online documenation and download at emboss.sourceforge.net.  Web interface for using EMBOSS at www.ebi.ac.uk/emboss/transeq/.
  8. Altschul, S.F., Gish W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.  Web interface and downloads at www.ncbi.nlm.nih.gov/blast/.
  9. Purves, Sadava, Orians, and Heller, 2005  Life: The Science of Biology, Freeman.  www.thelifewire.com.
  10. Gibas C and Jambeck P, 2001.  Developing Bioinformatics Skills, O'Reilly.
  11. Ewan Birney, Richard Copley, EMBL - European Bioinformatics Institute.  Wise2 at www.ebi.ac.uk/Wise2/index.html.
  12. Schwartz R L, Phoenix T, and Joy B D, 2005.  Learning Perl, Fourth Edition, O'Reilly Media, ISBN 0-596-10105-8.
  13. Comprehensive Perl Archive Network a cpan.org is a web site providing information on Perl and downloads for many platforms.  The LWP::simple module is described search.cpan.org/~gaas/libwww-perl-5.805/lib/LWP/Simple.pm.
  14. O'Reilly Perl site at perl.com.  Perl interpreter downloads are at http://www.perl.com/download.csp#binary.
  15. BioPerl web site at www.bioperl.org.  The site includes resources for getting, installing, and using BioPerl.
  16. Sun Microsystems Java web site at java.sun.com/.  The lates JDK can be downloaded at java.sun.com/javase/downloads/index.html and the Java Tutorial can be followed at java.sun.com/docs/books/tutorial/index.html.
  17. National Center for Supercomputing Applications at the University of Illinois at Urbana - Champaign, CGI documentation is at http://hoohoo.ncsa.uiuc.edu/cgi/.
  18. Stein L D, CGI Perl Module, CGI.pm at http://search.cpan.org/dist/CGI.pm/.  The basic CGI class is described at http://search.cpan.org/dist/CGI.pm/CGI.pm.
  19. Ensembl - joint project between EMBL - EBI and the Sanger Institute at http://www.ensembl.org/index.html. The Sanger Institue Vertebrate Genome Annotation (VEGA) database browser is at vega.sanger.ac.uk/index.html.
  20. San Diego Supercomputer Center Biology Workbench at workbench.sdsc.edu/.
  21. The Broad Institute at www.broad.mit.edu/.  The software page is at www.broad.mit.edu/tools/software.html and the data page is at www.broad.mit.edu/tools/data.html.
  22. Boulder Data Interchange Format home page at http://stein.cshl.org/boulder/ includes biological subclasses for Blast, GenBank, Medline, SwissProt, Unigene, and Omim (Online Mendelian Inheritance in Man).
  23. Apache Foundation, Tomcat website at tomcat.apache.org.
  24. Biodirectory.com at http://biodirectory.com web site has a list of bioinformatics tools and projects at http://www.biodirectory.com/directory/Top/Informatics_230.html (was Bioinformatics.org http://bioinformatics.org/search/fullprojectlist.php).
  25. US National Cancer Institute, Cancer Bioinformatics Infrastructure Objects (caBIO) project at ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/caBIO.
  26. Human Genome Organization (HUGO) Gene Nomenclature Committee web page at www.gene.ucl.ac.uk/nomenclature/.  The list of named human genes can be downloaded at www.gene.ucl.ac.uk/nomenclature/data/gdlw_index.html.
  27. Institute of Medical Genetics in Cardiff, Human Gene Mutation Database at http://www.hgmd.cf.ac.uk/ac/index.php.
  28. Griffiths A J F, Wessler S R, Lewontin R C, Gelbart W M, Suzuki D T, and Miller J H, 2005.  Introduction to Genetic Analysis, 8th Edition.  Freeman.  Also on the web at www.ncbi.nlm.nih.gov/books/.
  29. Schwartz R L, foy b d, and Phoenix T, 2006.  Intermediate Perl, 2nd Edition.  O'Reilly.
  30. Free Software Foundation, GNU emacs page at www.gnu.org/software/emacs/emacs.html.
  31. Kernighan B W and Ritchie D M, 1988.  The C Programming Language, Second Edition, Prentice Hall.
  32. Free Software Foundation, GNU C Compiler gcc at gcc.gnu.org/.
  33. Altschul S. F. , Madden T. L., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 1997, Vol. 25, No. 17 3389–3402. Oxford University Press. Available online at at pubmed.
  34. National Center for Biotechnology Information (NCBI), BLAST page at www.ncbi.nlm.nih.gov/blast/index.shtml.  The Statistics of Sequence Similarity Scores page is at www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html.   Executables of BLAST software can be downloaded at www.ncbi.nlm.nih.gov/blast/download.shtml.  BLAST databases may downloaded from ftp.ncbi.nlm.nih.gov/blast/db.
  35. Achour M., Betz F, et al, 2006.  PHP Manual at www.php.net/manual/en/index.php.
  36. Mozilla Developer Center.  AJAX: Getting Started at developer.mozilla.org/en/docs/AJAX:Getting_Started.
  37. Jason Cranford Teague, 2007.  CSS, DHTML, and AJAX.  The book's web site is at webbedenvironments.com/css_dhtml_ajax/.
  38. Crane D., Pascarello E., and James D., 2006.  Ajax in Action.  Manning Publications Inc.
  39. Sun Microsystems.  J2EE Version 1.5 Application Programming Interfaces are at java.sun.com/j2ee/1.5/docs/api/ and The Java Server Pages Specification is at java.sun.com/products/jsp/reference/api/index.html.
  40. The MySQL web site is at at www.mysql.com. MySQL Documentation is at dev.mysql.com/doc/index.html. The JDBC driver reference is at dev.mysql.com/doc/refman/5.1/en/connector-j.html.
  41. The PostgreSQL web site is at www.postgresql.org.
  42. Oracle's web site is at www.oracle.com.
  43. Microsoft's developer web site is at msdn.microsoft.com. A useful direct link is The C# Programming Guide, the top level of the C# section of the MSDN library. Another good development reference from Microsoft is www.asp.net, the official Microsoft web site for the .NET platform. There is a QuickStart Tutorial on building a web application with ASP.NET at quickstarts.asp.net.
  44. The Caucho Resin Application Server product page is at http://www.caucho.com/.
  45. The Hibernate web site is at www.hibernate.org/.
  46. The BioPHP web site is at biophp.org/.
  47. The csharpcomputing web site is at csharpcomputing.com/Tutorials/TOC.htm.
  48. The web site for Genome Viewer developed by Anton Zamov at MetaGen is at zamov.online.fr/projects/genome_viewer/.
  49. Ariel Dolan's Bioinformatics Tools web site is at www.aridolan.com/biq/Intro.aspx.
  50. Sklar and Trachtenberg, 2006. PHP Cookbook, O'Reily.
  51. The Apache HTTP Server is at httpd.apache.org. Other useful documents on the site are Apache Tutorial: Dynamic Content with CGI and Using Apache with Microsoft Windows.
  52. The BEA WebLogic Product Family web page is at bea.com.
  53. The Eclipse project is at www.eclipse.org. The Web Tools Project home page is at http://www.eclipse.org/webtools/main.php.
  54. The Apache Struts project is at struts.apache.org.
  55. The Spring project is at springframework.org. The Spring Web Flow subproject is at www.springframework.org/webflow.
  56. Fielding, Roy Thomas, 2000. Architectural Styles and the Design of Network-based Software Architectures. DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Information and Computer Science, UNIVERSITY OF CALIFORNIA, IRVINE. Online at www.ics.uci.edu/~fielding/pubs/dissertation/top.htm.
  57. The Apache Axis 2 project web site is at ws.apache.org/axis2/.
  58. The Direct Web Remoting project web site is at dwr.dev.java.net/.
  59. The BioJava project web site is at biojava.org/wiki/Main_Page.
  60. The Apache Commons web site is at jakarta.apache.org/commons/. The FileUpload web page is at jakarta.apache.org/commons/fileupload/.
  61. Sklar D. and Trachtenberg A., 2006. PHP Cookbook. O'Reily.
  62. Some useful direct links at php.net are: Mailing Lists, PEAR - PHP Extension and Application Repository, PEAR Channels, and PECL is a repository for PHP Extensions.
  63. The PHP Knowledge Base is at www.faqts.com/knowledge_base/index.phtml/fid/51/.
  64. The PHP Dev Center is at www.onlamp.com/php.
  65. The Planet PHP web site is at www.planet-php.net.
  66. The Zend Developer Zone web site is at devzone.zend.com.
  67. The phpDocumentor web site is at www.phpdoc.org.
  68. Crocker, D., 1982. RFC 822 - STANDARD FOR THE FORMAT OF ARPA INTERNET TEXT MESSAGES. Internet Engineering Task Force, online at www.faqs.org/rfcs/rfc822.html.
  69. Resnick, P. (Editor), 2001. RFC 2822 - Internet Message Format. Internet Engineering Task Force, online at www.faqs.org/rfcs/rfc2822.html.
  70. Henderson, C. Parsing Email Adresses in PHP. Online at www.iamcal.com/publish/articles/php/parsing_email. Cal has a collection of articles at www.iamcal.com/publish and PHP code available for download at code.iamcal.com/php/rfc822/.
  71. Libgd web site at libgd.org.
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© 2006-2007 Alex Amies