StrBio java class libraries Files

StrBio version 1.3

SUMMARY:

The StrBio library (StrBioLib) is a set of Java classes useful for
development of software for computational structural biology
research. They are licenced under the LGPL (see LICENSE.txt for
details).

These classes are the basis for several published research projects,
including the Pred2ary secondary structure prediction program and the
ASTRAL database of protein domain sequences.

The most interesting structural biology applications included are:
    * Pred2ary protein secondary structure prediction [1]
    * JThread protein fold prediction [2]
    * ConvertProtein for interconversion of protein file formats
      (FASTA, PDB, MSF, ALN, CASP, DSSP, HSSP, YAPF)
    * Filters to exchange data with commonly used molecular biology
      applications (e.g., BLAST, MinArea, MODELLER, MUSCLE, Primer3)
    * MakeRAF tool to create the Rapid Access Format sequence maps for
      the ASTRAL database. [3], http://astral.berkeley.edu

Other more general-purpose functionality that is included:
    * Neural network library, including Scaled Conjugate Gradient or
      Steepest Descent optimization
    * Hooke and Jeeves derivative-free global optimization algorithm
    * Misc mathematical objects and algorithms (vectors, matrices, etc)
    * Efficient string formatting using Printf-based syntax (printf,
      atoi, atof, etc.)

References:

[1] - Chandonia JM, Karplus M. 1999. New methods for accurate
     prediction of protein secondary structure. Proteins 35:293-306.
[2] - Chandonia JM, Cohen FE. 2003. New local potential useful for
    genome annotation and 3D modeling. J Mol Biol 332:835-50.
[3] - Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M,
    Brenner SE. 2004. The ASTRAL Compendium in 2004. Nucleic Acids Res
    32 Database issue:D189-92.


INSTALLATION:

Requires working Java and either GNU Make or Apache Ant software to be
installed.

Set your classpath to include the src and test directories under this
one.

Depending on whether you prefer Make or Ant, follow one of the
following sets of instructions:

Installation using GNU Make:

"make" to build class files and API documentation.
You can then view the documentation with a web browser pointed at the
javadocs directory.

"make test" to run unit tests (requires JUnit 4), or
"make oldtest" to run unit tests with JUnit 3.

"make jars" to build stand-alone jar files (see below)

"make install" to copy the jar files to the default location
 (/usr/local/lib).

Installation using Apache Ant:

"ant compile" to build class files.

"ant javadocs" to build API documentation.
You can then view the documentation with a web browser pointed
at the javadocs directory.

"ant test" to run the unit tests.

"ant jars" to build stand-alone jar files (see below)

"ant install" to copy the jar files to the default location
 (/usr/local/lib).


USE:

Several jar files are created under lib/:

makeraf.jar - Contains the stand-alone program MakeRAF, for
  creating RAF files (of interest to ASTRAL users).

pred2ary.jar - Contains the stand-alone program Pred2ary, for
  secondary structure prediction.

strbio.jar - Contains all the class files, for use in other
  programs.  Put this in your CLASSPATH if you're developing
  software that extends StrBioLib.


GETTING STARTED:

There are samples demonstrating both how to use the stand-alone
programs and how to code with StrBioLib under examples/.  Most example
directories have README.txt files explaining the contents.  The
examples/cookbook/ directory has files containing code snippets; each
file name describes the content.


MAILING LIST:

The "strbio-devel" list is for discussion among developers and users
of the code.  If there is sufficient demand, we can split off other
lists.  The mailing list is hosted on SourceForge:
  http://lists.sourceforge.net/mailman/listinfo/strbio-devel


SUBVERSION REPOSITORY:

There is now a public Subversion repository for the project, hosted
by Sourceforge.  You can browse changes to the code here:
    http://sourceforge.net/p/strbio/code/HEAD/tree/

To check out the very latest (possibly broken) version of the code,
install Subversion and do:
      svn co https://svn.code.sf.net/p/strbio/code/trunk strbiolib


COMPATIBILITY:

StrBioLib 1.3 requires Java 1.3 or higher, due to the need for
Program to run some subprocesses in their own subdirectory.  This was
required to interface with some poorly behaved programs that spew
dozens of temporary files all over the current working directory.

The unit tests have been run with JUnit 3.8 (required to test older
versions of Java) and Junit 4.


REFERENCE:

If you publish research in which you used StrBioLib, please cite:

Chandonia, JM.  2007.  StrBioLib: a Java library for development of
custom computational structural biology applications.  Bioinformatics,
May 30, doi: 10.1093/bioinformatics/btm269.