#acl All:read == BRAIN Project == The Biologically Relevant Analysis of Interaction Networks (BRAIN) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g. from protein chip or phage display experiments). BRAIN can be accessed as a Cytoscape plugin which reads peptide binding profiles and generates interactions displayed as a Cytoscape network. <> BRAIN consists of a library or API, and of a Cytoscape plugin. === BRAIN Library === The BRAIN library holds the algorithms and methods for interaction prediction. This library is required to build the BRAIN plugin. === BRAIN Plugin === The BRAIN plugin is a way of running various BRAIN algorithms from the Cytoscape user interface. The plugin runs a prediction analysis and presents the results visually as an interactive Cytoscape network. ---- == Downloads == The BRAIN library and plugin are available below for download as Java archive (JAR) files and Java source tree tarballs. === Latest Release === ''BRAIN Library'': Version 1.4 (April 11, 2012) <
> Build: [[attachment:brainlib-1.5.jar]] <
> Source: [[attachment:brainlib-1.5-src.zip]] ''BRAIN Plugin'': Version 1.0.5 alpha (May 23, 2007) <
> Build: [[attachment:brainPlugin.jar]] <
> Source: [[attachment:BRAIN-Plugin-1.0.5-src.tgz]] ''Dependencies'': Additional JARs required by BRAIN - [[attachment:brainDeps.tar.gz]] === Earlier Releases === ''BRAIN Library'': Version 1.4 (September 29, 2008) <
> Build: [[attachment:brainlib-1.4.jar]] <
> Source: To be posted by October 3, 2008 ''BRAIN Library'': Version 1.3 (May 12, 2008) <
> Build: [[attachment:brainlib-1.3.jar]] <
> Source: [[attachment:BRAIN-Library-1.3-src.tgz]] ---- == Installing the Plugin == === System Requirements === * Java Runtime Environment (JRE) 1.5 or later * [[http://www.cytoscape.org|Cytoscape]] 2.4.1 or later === Installation === * Place ''brainPlugin.jar'' and ''brainlib_1.1.jar'' in the Cytoscape ''plugins'' directory (located in the Cytoscape program directory, e.g. /usr/local/bin/Cytoscape or C:\Program Files\Cytoscape_v2.4.1) * Extract and place all files from brainDeps.tar.gz into the Cytoscape ''plugins'' directory * Launch Cytoscape * Look in the ''Plugins'' menu for the ''BRAIN'' item. If you don't see it there, revisit the above steps to make sure all files are in the right place. ---- == Running the Plugin == * Launch Cytoscape * Set analysis parameters from ''Plugins > BRAIN > Set Parameters'' * Start the BRAIN analysis from ''Plugins > BRAIN > Run BRAIN'' ---- === Notes on Using BRAIN === BRAIN takes one or more query proteins and their respective peptide ligands, builds a PWM-based profile for each protein, searches a protein sequence database for similar profiles, and returns a ranked set of proteins that are predicted to interact with the query proteins. A query protein and its experimentally determined peptide ligands are represented as a [[/PeptideFile|peptide file]], in which the peptide binders are listed as an ungapped multiple sequence alignment. The plugin can open a single peptide file, or multiple peptide files that are grouped into a [[/PeptideFile#ProjectFiles|project file]]. From a peptide file, BRAIN generates a position weight matrix (PWM), or protein profile. The profile constitutes the distributions of amino acids (rows) at each of the positions (columns) of the peptide pattern. In a given column of the PWM, each amino acid is assigned a weight based on its frequency of occurrence at the given position. These weights are normalized to 1.0 to emulate probabilities of occurrence. BRAIN searches a protein sequence database (in FASTA, Swiss``Prot, Gen``Pept, or EMBL format) for the pattern represented by the protein profile. An interaction score (p-value) is calculated for each hit, and all hits exceeding the user-provided score threshold are reported as predicted interactors of the query protein. The output is provided as a Cytoscape network, enabling further graph-based analysis and exploration of node (protein) and edge (interaction) attributes including interaction score, gene name, motif sequence, and associated OMIM or Morbid``Map record (if available). ---- == Release Notes == '''BRAIN Library 1.5''' (April 11, 2012) * Supports loading of PWM files into !ProteinProfile object * Minor changes to support organism member variable in !ProteinProfile object '''BRAIN Library 1.4''' (September 29, 2008) * Supports the Cytoscape Task API to display a progress bar during logo tree generation '''BRAIN Library 1.3''' (May 12, 2008) * Single linkage hierarchical clustering used to cluster profiles for generating logo tree * Sequence logo alignment algorithm added for generating logo trees * New code for amino acid grouping and coloring schemes to be defined, e.g. for generating sequence logos and logo trees '''BRAIN Library 1.2''' (February 2008) * Internal release for alpha-testing '''BRAIN Library 1.1''' (July 26, 2007) * Added PDZ symbol style for PDZ type residue colouring in sequence logo generation code (required by LoLA tool) '''1.0.6''' (June 12, 2007) * brain.jar: Ability to retrieve additional database references from Protein``Profile object (previously was only able to retrieve the first ID in the Accession field of the peptide file). '''1.0.5''' (May 23, 2007) * Code reorganization: brainPlugin.jar now holds only those classes related to the Cytoscape plugin. All other code has been moved to a new Brain Library project. '''1.0.4''' (May 15, 2007) * Network node can represent a single domain or a protein containing multiple domain instances (via new Advanced Options tab) * Lower scoring motif hits are now reported * New node attribute ''Domain Name'' to hold a semantic domain identifier (Gene Name + Domain Number, for now) '''1.0.3''' (April 23, 2007) * Support for new peptide file format version 1.1 (and back-compatible with format version 1.0) * New node attributes ''Sequence Start'', ''Sequence Stop'', ''Comment'' for profiles generated from new peptide file format '''1.0.2''' (April 11, 2007) * Report SNPs for entire protein sequence and for domain subsequence only. * Option to specify codon bias file * Option to load unique peptides only from peptide file(s) '''1.0.1''' (February 21, 2007) * Port to Cytoscape API 2.4 and Java SE 5.0 ---- == Future Developments == (in order of priority) 1. Regular expression filtering of profile search results. 1. Expose auto-score threshold functionality in Profile Search panel (allow the user to specify automatic score threshold setting instead of having to specify a score threshold themselves). 1. Expose "regex" search features - new Pattern Search panel similar to Profile Search 1. New feature: consider aa groups in PWM searching 1. Design an improved scoring scheme (e.g. take into account surface accessibility) and drop down box to select different scores. ---- == Contact == If you have any questions or feedback, please email Moyez Dharsee at mdharsee@infochromics.com.