The BioJava Tutorial

Description

The BioJava Tutorial
BioJava is a library of open source classes intended as a framework for applications which analyse or
present biological sequence data. This tutorial illustrates the core sequence-handling interfaces available
to the application programmer, and explains how BioJava differs from other sequence-handling libraries.
For more comprehensive descriptions of the BioJava API, please consult the JavaDoc documentation.
1. Symbols and SymbolLists
2. Sequences and Features
3. Sequence I/O basics
4. ChangeEvent overview
5. ChangeEvent example using Distribution objects
6. Implementing Changeable
7. Blast-like parsing (NCBI Blast, WU-Blast, HMMER)
8. walkthrough of one of the dynamic programming examples
9. Installing BioSQL
The BioJava tutorial, like BioJava itself, is a work in progress, and all suggestions (and offers to write
extra chapters ;) are welcome. If you see any glaring errors, or would like to contribute some
documentation, please contact Thomas Down or the biojava-l mailing list.
http://www.biojava.org/tutorials/index.html [02/04/2003 13.39.36]BioJava.org - Main Page
BioJava.org
Open Bio sites About BioJava
The BioJava Project is an open-source project dedicated to providing Java toolsbioperl.org
for processing biological data. This will include objects for manipulatingbiopython.org
sequences, file parsers, CORBA interoperability, DAS, access to ACeDB,bioxml.org
dynamic programming, and simple statistical routines to name just a few things ...

Sujets

• Interfaceur (astronautique)
• Alphabet copte
• Algèbre de Clifford
• Distille
• SSE3
• Rolls-Royce Limited

Informations

• Publié par: Ewlo
• Nombre de lectures: 101
• Langue: English

Extrait

The BioJava Tutroail Java TutThe Bio

BioJavais a library of open source classes intended as a framework for applications which analyse or present biological sequence data. This tutorial illustrates the core sequence-handling interfaces available to the application programmer, and explains how BioJava differs from other sequence-handling libraries. For more comprehensive descriptions of the BioJava API, please consult theJavaDoc documentation. 1.Symbols and SymbolLists 2.Sequences and Features 3.Sequence I/O basics 4.ChangeEvent overview 5.ChangeEvent example using Distribution objects 6.Implementing Changeable 7.Blast-like parsing(NCBI Blast, WU-Blast, HMMER) 8.walkthrough of one of the dynamic programming examples 9.Installing BioSQL The BioJava tutorial, like BioJava itself, is a work in progress, and all suggestions (and offers to write extra chapters ;) are welcome. If you see any glaring errors, or would like to contribute some documentation, please contactThomas Downor thebiojava-lmailing list.

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About BioJava The BioJava Project is an open-source project dedicated to providingJavatools for processing biological data. This will include objects for manipulating sequences, file parsers, CORBA interoperability,DAS, access toACeDB, dynamic programming, and simple statistical routines to name just a few things. The BioJava library is useful for automating those daily and mundane bioinformatics tasks. As the library matures, the BioJava libraries will provide a foundation upon which both free software and commercial packages can be developed. News 12 th at ook    e n c o eD i r t e c b e m l eka o T c l     f a o   olc   B o i k o b J o a o v k a - i s n t   y A le n d ge o r for ,  BioJ w nt e a w  t a i   o n n    ucem  wtesieb .av a a h it An experimental forum/blog has been set up. It may not be 30 th  always or it may migrate to another platform/hostOctober there eventually. You can find ithere 23 th sror.nippre g ug A Jaio t B us  22.1 avdesaelergfix, bu Seq forIe r Oeucn t-iruodn BioJava 1.21 released, including BioSQL support, for 14 th March general purpose storage of sequence data in a relational database. BioJava 1.20 is ready, featuring improved sequence and 13 th Feb y  parsers, faster dynamic programming routines, client blast ruar libraries  for DAS 1.0, and much more. Take a look atthe change logor go straight to thedownload area There is going to be a repeat of last year's successful `BioJ boot camp' workshop, held at the Wellcome Trust 6 th ook va a roF .egdirbmaC r ls,iltadee or m y ar0220 Frue G b nemo eaCpmsun ae here Getting a copy of the project

Open Bio sites bioperl.org biopython.org bioxml.org biodas.org biocorba.org Documentation Overview Getting started Tutorial BioJava in Anger JavaDoc API Demos WikiDocs Bug Tracking Web Interface Mailing List biojava-l Archive Mail us Subscribe Mailing List biojava-dev Archive Mail us Subscribe Forum (experimental) Participants Download WebCVS

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BioJava is distributed underLGPL. This means that you can use the libraries without your software being forced under either theLGPLorGPL.LGPLisnot GPL. BioJava releases can be obtained by FTP from ourdownload area. Instructions for installing the library, and building source releases, can be found on the Getting startedpage. You can also maintain an up-to-date view of BioJava with CVS. We provide anonymous CVSserver. If you wish to contribute your existing code or help maintain part of the BioJava code-base, then we can supply you with a read/write account. Documentation The overalldesign ethosof BioJava is probably the best place to start, as it explains how BioJava is structured. The currentJavaDoc apireference should provide up-to-date api documentation. Many of thedemonstration programshave some description, both as to their purpose, and how to run them. There is also a shorttutorialon sequence handling in BioJava. Thanks This site could not exist without the donations of bandwith and hardware from Genetics Institute, Inc.and theCompaq Bioinformatics Solutions Center. In addition, we would like to thank Chris Dagdigian for maintaining the bio* servers.

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