|CRT home > Residue-based Diagram generator (RbDg)|
|[ description ]|
RbDg is a program that generates residue-based diagrams of proteins. RbDg can be thought of as a batch version of RbDe (the residue-based diagram editor), with added features. Added features include the ability to generate diagrams for different protein families. The layout of the different secondary structure elements of a protein is configured through an input file. This makes RbDg very useful to produce diagrams of proteins for databases such as GPCRDB or NuclearDB.
Usage of RbDg is summarized on the following Figure:
Generating diagrams of proteins with RbDg requires three steps.
Step 1 assembles the definition of the layout of the subunits with the sequence and residue properties to display on the diagram.
Step 2 processes input files to produce diagram images in the graphics formats supported by RbDg and creates an XML output.
Step 3 converts the XML output of RbDg to an HTML file that includes the diagram images.
Each step is further documented below.
|[ about the method ]|
The algorithms used to render the diagrams were described in F. Campagne and H. Weinstein.
Schematic representation of residue-based protein-context dependent data: an application to transmembrane proteins.
1999. J. of Molecular Graphics and Modeling, 17(3-4):207-13
|[ documentation ]|
RbDg can be started with the command $CROVER/bin/rbdg -i input.xml to process one input file, or can process a list of input files with the command $CROVER/bin/rbdg -list list-of-inputs. The latter option provides important speedups when multiple diagrams are being generated.
The input file is an XML file that adheres to specific conventions (described in an XML schema). The schema for the input file is described here:
When RbDg processes input files, it produces output files according to the instructions given in the input. RbDg can create images in GIF or SVG format. SVG is a vectorial format, and thus can produce high-quality illustrations when printed. (SVG can also be imported in Illustrator 10+ to edit the diagrams, add annotations, etc.). Example of images produced with RbDg are shown below (SVG format may require a plugin):
RbDg also produces an XML output file, that documents the file produced by the command and can be transformed to HTML. This is intended to allow database curators to customize the look and feel of the page that presents the diagrams to match aesthetic conventions of the database. Schema, documentation and a sample output file are provided here:
RbDg output can be transformed with XSL templates to produce HTML files (other formats are possible also). The following shows a sample template and the HTML output that it produces:
|[ availability ]|
RbDg is used to create diagrams for several biological databases (for instance GPCRDB, PDZBase, Arcadia, GPCR Natural Variants database and TRansporter Annotation Center (TRAC)).
RbDg is distributed under a license. The license is free of charge for academic institutions to use in support of education and academic research, provided that the diagrams generated with RbDg are made available at no charge to the research community. For more information about RbDg, please contact Fabien Campagne.
Apr, 2013; Christopher E. Mason, Assistant Professor in PBSB Program, was featured in Reuters, Nature, Newsday, CBC news, Huffington Post, The New Yorker, The Washington Post, and other media outlets for his recent paper on gene patents published in Genome Medicine and also for his work as a scientific expert on gene patents for the AMP v. Myriad Genetics case before the US Supreme Court.|
Apr, 2013; Sheng Li, a PBSB graduate student in Dr. Christopher E. Mason's lab, won a National Science Foundation Travel Fellowship and was invited to give a speech at the 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013) held at the Tsinghua University for her paper on "An optimized algorithm for detecting and annotating regional differential methylation".
Mar, 2013; Two Graduate Students working with PBSB faculty were awarded competitive graduate research fellowships: (1) Lenore Pipes, a graduate student in the Tri-Institutional Graduate Program in Computational Biology and Medicine, working in the laboratories of Dr. Christopher E. Mason and Dr. Adam Siepel, won a 2013 National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) Fellowship for her work on de novo transcriptome assembly and genome assembly. Her fellowship will last from 2013-2016. (2) Michael LeVine, a PBSB graduate student working in the lab of Dr. Harel Weinstein was awarded a National Research Service Award (NRSA - F31) to work on "Ligand-Specific Allosteric Modulation by Drugs of Abuse" for the next 4 years, starting June 1, 2013.
Jan, 2013; Dr. Olivier Elemento was awarded a five-year Irma T. Hirschl Career Scientist Award.
Dec, 2012; Mr. Vaja Liluashvili, a visiting graduate student in the Gumus laboratory was awarded a Sao Paulo Research Foundation (FAPESP) full fellowship to present at the international meeting SPAS: Advances in Molecular Oncology: Translating Molecular Biology into Cancer Treatment in Sao Paulo, Brazil 3-8th February 2013. Mr. Liluashivili will present his research with Dr. Zeynep H. Gumus, titled "iCAVE: immersive 3D visualization of complex biomolecular interaction networks".
Sept, 2012; The Campagne laboratory was awarded the best poster award for "Compression of high-throughput sequencing data" at the Wellcome Trust's Genome Informatics 2012 meeting in Cambridge, UK.
May, 2012; Dr. Christopher Mason was featured in a two part profile by the New York Genome Center for his work on non-human primate genomics, gene patenting policy, and other activities.
March, 2012; Michelle Sahai, Ph.D., a Postdoctoral Associate in Harel Weinstein's lab, was awarded a three year Canadian Institutes of Health Research (CIHR) Fellowship for her research on Molecular Mechanisms of the Dopamine Transporter Function: The effects of drugs of abuse.
Feb, 2012; Sayan Mondal, a student in Harel Weinstein's lab, won the Student Research Achievement Award at the Biophysical Society's 2012 Annual Meeting for his poster on the interaction of GPCRs with the membrane.
Jan, 2012; Jan Dlabal, a student from the Lycée Français de New York, was selected as a semi-finalist in the 2012 Intel Science Talent Search, for work on the determination of large-scale genomic structure performed in the lab of Olivier Elemento.
Oct, 2011; Sheila Nirenberg presented a talk, "Can we speak the language of the brain?", at the TEDMED 2011 conference.
A Q & A session followed.
Nov, 2011; GobyWeb binary release. The Campagne laboratory has just released a binary distribution of GobyWeb. This first public release of GobyWeb makes it possible to install the tool locally for non-commercial use. Detailled installation instructions are available on the download page.
Apr, 2011; Dr. Olivier Elemento was awarded an NSF CAREER Grant, the National Science Foundation's most prestigious award in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research.
Nov, 2010; Dr. Sheila Nirenberg's work on artificial retinas has been featured in Technology Review, Wired, Scientific American, and the New Scientist.
Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
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