Overview

Bio::BioStudio

SEE ALSO
	
	Bio::GeneDesign

DEPENDENCIES

The Perl libraries not in the Perl core that BioStudio requires are Text::Diff, 
Time::Format, Exception::Class, Digest::MD5, URI::Escape, Readonly, and 
YAML::Tiny. All of these perl libraries can be installed by BioStudio at install 
time or beforehand with cpan.

You need BioPerl-live, from github and not from cpan.
  git clone https://github.com/bioperl/bioperl-live.git
  cd bioperl-live/
  sudo perl Build.PL
  sudo ./Build installdeps
  sudo ./Build test
  sudo ./Build install
  cd ../
  git clone https://github.com/bioperl/bioperl-run.git
  cd bioperl-run/
  sudo perl Build.PL
  sudo ./Build installdeps
  sudo ./Build install

OPTIONAL PACKAGES

If a graphical user interface is desired, the excellent GBrowse2 is available 
and easily installed from https://github.com/GMOD/GBrowse.

For static graphic representations of chromosomes BioStudio requires the Cairo 
library and FreeType2 as well as the associated perl bindings Cairo and 
Font::FreeType.

BLAST+ is required for sequence comparison and for PCRTag generation. Make sure 
you are using BLAST+ and not any older set of BLAST scripts. The package is 
available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/.

BioStudio can use certain secondary structure prediction algorithms to improve 
primer design. It can use UNAFold (http://www.ibridgenetwork.org/rpi/unafold) 
UNAFold (low cost for academic users) or the older, slower, but freely available 
MFold (http://mfold.rna.albany.edu/?q=mfold/download-mfold). If you do use 
UNAFold, you may want to also download the Mfold utilities 
(http://mfold.rna.albany.edu/download/mfold_util-4.7.tar.gz), which enable pdf 
visualization of secondary structures. 

BioStudio's performance on large genomes is drastically improved by the indexing 
annotations in a relational database. MySQL 5.6 or Postgres 9.3 are supported. 
Make sure to install the perl libraries DBI and either DBD::mysql or DBD::Pg.

INSTALLATION

To install this module, run the following commands:

	perl Build.PL
	./Build
	./Build test
	./Build install

SUPPORT AND DOCUMENTATION

After installing, you can find documentation for this module with the
perldoc command.

    perldoc Bio::BioStudio

You can also look for information at:

    RT, CPAN's request tracker (report bugs here)
        http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio::BioStudio

    AnnoCPAN, Annotated CPAN documentation
        http://annocpan.org/dist/Bio::BioStudio

    CPAN Ratings
        http://cpanratings.perl.org/d/Bio::BioStudio

    Search CPAN
        http://search.cpan.org/dist/Bio::BioStudio/

FUTURE WORK

  •Revamp the custom feature system so that they are described in individual
	files and stored as Bio::Root::Root objects (in concert with BioStudio)
	

LICENSE AND COPYRIGHT

Copyright (C) 2011 Sarah Richardson

This program is distributed under the (Revised) BSD License:
L<http://www.opensource.org/licenses/bsd-license.php>

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:

* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.

* Neither the name of Sarah Richardson's Organization
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.