NAME
   InSilicoSpectro - Open source Perl library for proteomics

INSILICOSPECTRO PROJECT DESCRIPTION
   This is the description of the entire InSilicoSpectro project; a
   description of the InSilicoSpectro.pm module is provided hereunder.

   InSilicoSpectro is a proteomics open-source project intended to cover
   common operations in mass list file format conversions, protein sequence
   digestion, theoretical mass spectra computations, theoretical and
   experimental MS data matching, text/graphic display, peptide retention
   time predictions, etc.

   The problems of raw data processing, storage and database searching are
   not addressed by the InSilicoSpectro project. InSilicoSpectro is
   released under the LGPL license and it is available from a dedicated web
   site at http://insilicospectro.vital-it.ch.

   The general design of the modules follows the object oriented
   programming (OOP) model and most of the modules are class definitions
   actually. The module that implements most of the theoretical mass
   computation routines supports a dual OOP and procedural programming
   model. InSilicoSpectro modules make use of some Perl modules that are
   not part of the standard Perl distribution, such as
   Statistics:Regression, XML:Twig, GD, and IA:NNFlex.

   We have developed a simple and minimal hierarchy to represent protein
   sequences and peptides (as digestion product) in a way that, on the one
   hand, fits the needs of the computations we perform and, on the other
   hand, stays relatively neutral in its design. Thus it should be possible
   to combine the latter classes with existing projects at users sites,
   e.g. via multiple inheritance, or to use them as the basis of more
   sophisticated objects.

   InSilicoSpectro Perl code is documented mainly via pod and a wide
   collection of simple and focused examples. An introductory explanation
   is provided here to guide new users and give them an understanding of
   the library that should be sufficient such that pod and the examples are
   the only necessary documentation.

 Installation
 Library organization
   InSilicoSpectro modules (lib/InSilicoSpectro) are organized according to
   their function. At the more general level there is a module named
   InSilicoSpectro.pm (This one!!) that provides general functionalities
   for initializing all other modules. More specialized modules are grouped
   in three folders:

   Spectra, for mass list-related;
   InSilico, for computational modules;
   Utils, for a few utility modules.

   In addition, illustrative examples can be found in three folders:

   scripts, which contains a set of tools implemented with InSilicoSpectro
   modules;
   cgi, which contains scripts implementing a simple web-based set of
   tools;
   t, which contains test programs that are examples as well.

   Now, by considering the main topics we cover in InSilicoSpectro one
   after another, we introduce the main modules and examples the user
   should try and look at to gain autonomy with the whole library.

 Mass list file format conversion
   A general purpose conversion program, convertSpectra.pl in folder
   scripts, allows you to convert one mass list format to another. A CGIzed
   version exists in the cgi folder: cgiConvertSpectra.pl.

   convertSpectra.pl is a good starting point to see a high-level usage of
   the basic methods implemented in the underlying modules.

   InSilicoSpectro::Spectra::ExpSpectrum is the basic class for
   representing spectra, i.e. a list of peaks (namely a list of pointers to
   peaks). Peaks are represented as list of attributes such as mass,
   intensity, SN, etc. The order of the attributes in these lists is given
   by an object of class InSilicoSpectro::Spectra::PeakDescriptor. See
   t/Spectra/testExpSpectrum.pl and t/Spectra/testPeakDescriptor.pl.

   By means of classes InSilicoSpectro::Spectra::MSSpectra,
   InSilicoSpectro::Spectra::MSMSSpectra,
   InSilicoSpectro::Spectra::MSMSCmpd, and InSilicoSpectro::Spectra::MSRun
   we represent PMF (MS) and MS/MS spectra, and HPLC runs. See
   t/Spectra/testSpectra.pl.

 Utils
   The module InSilicoSpectro::Utils::IO.pm contains miscellaneous
   utilities for accessing compressed files, defining a common verbose
   variable, etc.

 pI estimations
   scripts/computePI.pl is a tool that exemplify the usage of the class
   InSilicoSpectro::InSilico::IsoelPoint. Examples of how to use it can be
   found in t/InSilico/examples_rt_pi. See also the example in
   t/InSilico/testIsoelPoint.pl. A CGI version of computePI.pl can be found
   in cgi folder.

 Retention time prediction
   scripts/computeRT.pl is a tool that exemplify the usage of the class
   InSilicoSpectro::InSilico::RetentionTimer. Examples of how to use it can
   be found in t/InSilico/examples_rt_pi. See also the examples in
   t/InSilico/testPetritis.pl and t/InSilico/testHodges.pl. A CGI version
   of computeRT.pl can be found in cgi folder.

 Enzymes
   Enzymes are modeled by class InSilicoSpectro::InSilico::CleavEnzyme. See
   t/InSilico/testCleavEnzyme.pl.

 PTMs and other modifications
   Modifications of residues are modeled by class
   InSilicoSpectro::InSilico::ModRes. See t/InSilico/testModRes.pl.

 Protein and peptide sequences
   The basic class for biological sequences is
   InSilicoSpectro::InSilico::Sequence. We then define
   InSilicoSpectro::InSilico::AASequence to represent protein sequences
   with their modifications. A class InSilicoSpectro::InSilico::Peptide is
   used for enzymatic digestion products as we need special data in this
   case that are not part of a standard protein model.

   Examples can be found in t/InSilico: testSequence.pl, testAASequence.pl,
   testPeptide.pl.

 Protein digestion and mass computations
   The main module for digestion and mass computations is
   InSilicoSpectro::InSilico::MassCalculator. Examples of digestions and
   protein/peptide mass computations, including in the presence of
   fixed/variable modifications, are found in t/InSilico:
   testCalcDigest.pl, testCalcDigestOOP.pl, and testCalcVarpept.pl. OOP
   means an example with the OOP model as MassCalculator supports both an
   OOP and procedural interface.

 PMF
   The match between theoretical peptide masses and PMF experimental data
   is made by functions found in InSilicoSpectro::InSilico::MassCalculator.
   In the OOP model it is possible to represent PMF matches in objects of
   class InSilicoSpectro::InSilico::PMFMatch. See
   t/InSilico/testCalcPMFMatch.pl and t/InSilico/testCalcPMFMatchOOP.pl.

 Peptide fragmentation
   Theoretical fragment masses are computed by functions found in
   InSilicoSpectro::InSilico::MassCalculator. In the OOP model, theoretical
   MS/MS spectra can be represented as an object of class
   InSilicoSpectro::InSilico::MSMSTheoSpectrum, which represents in turn
   the various ions as InSilicoSpectro::InSilico::InternIonSeries and
   InSilicoSpectro::InSilico::TermIonSeries.

   The match between experimental and theoretical masses is also computed
   by InSilicoSpectro::InSilico::MassCalculator and in the OOP model the
   class InSilicoSpectro::InSilico::MSMSTheoSpectrum can store the match in
   addition to the theoretical spectrum.

   See in t/InSilico: testCalcFrag.pl, testCalcFragOOP.pl,
   testCalcMatch.pl, testCalcMatchOOP.pl, getIonIntensities.pl, ionStat.R.

 Graphical display of MS/MS spectra/matches
   The class InSilicoSpectro::InSilico::MSMSOutput instanciates objects
   aimed at providing different formats in order to represent MS/MS spectra
   and matches. See in t/InSilico: testMSMSOutText.pl, testMSMSOutLatex.pl,
   testMSMSOutHtml.pl, testMSMSOutPlot.pl, testMSMSOutLegend.pl.

 Mini web site
   In folder miniweb we provide a perl script build-miniweb.pl that builds,
   from CGI scripts in folder cgi, a simple web site for protein digestion,
   mass computations, and pI and retention time estimations.

MODULE DESCRIPTION
   The module InSilicoSpectro.pm comprises generic functions that are
   useful for the whole project.

FUNCTIONS
  saveInSilicoDef([$out])
   Saves all registered definitions into the configuration file named $out,
   e.g. insilicodef.xml

  getInSilicoDefFiles()
   Returns the list of configuration files given by the operating system
   environment variable, whose name is stored in
   $InSilicoSpectro::DEF_FILENAME_ENV (default "INSILICOSPECTRO_DEFFILE").

   The environment variable can point more than one file (separated by
   ':'), or be a glob ('...*...' expression).

  init([@files])
   Loads a list of configuration files given as parameter or the default
   configuration files as returned by getInSilicoDefFiles.

SEE ALSO
   InSilicoSpectro::InSilico, InSilicoSpectro::Spectra,
   InSilicoSpectro::Utils

COPYRIGHT
   Copyright (C) 2004-2005 Geneva Bioinformatics (www.genebio.com) &
   Jacques Colinge (Upper Austria University of Applied Science at
   Hagenberg)

   This library is free software; you can redistribute it and/or modify it
   under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation; either version 2.1 of the License, or (at
   your option) any later version.

   This library is distributed in the hope that it will be useful, but
   WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser
   General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with this library; if not, write to the Free Software Foundation,
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

AUTHORS
   Jacques Colinge, www.fhs-hagenberg.ac.at

   Alexandre Masselot, www.genebio.com

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