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|Apollo +||<span style="color:red">'''Please be aware that Berkeley Bioinformatics Open-Source Projects (BBOP) is no longer developing the desktop version of Apollo and that support for its use has been discontinued.'''</span> Apollo is a GUI (graphical user interface)-based tool for editing genome annotations. Like [[GBrowse]], Apollo allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off [[GFF3]] or a [[Chado]] database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. Apollo is a standalone Java application. +|
|BLAST Graphic Viewer +||BLAST Graphic Viewer provides a graphical visualization of the regions contained within HSPs relative to the query sequence. BLAST Graphic Viewer is also known as blastGraphic. +|
|BioMart +||Links to BioMart installations in the wild +, BioMart is a freely available, open source, federated database system that provides unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework. +|
|CMap +||Comparative mapping resource for grasses (plant) +, A publicly accessible legume resource that will integrate genetic and molecular data from multiple legume species and enable cross-species comparisons +, The Honey Bee genome database +, …|
|Canto +||Curate GO annotations for proteins using UniProtKB identifiers +, Canto is an online tool that supports functional gene annotation by community researchers as well as by professional curators. It provides a simple interface to gather genetic and molecular data from publications for inclusion in public biological databases. Canto employs OBO ontologies to ensure a consistent vocabulary is used to describe gene and gene product functionality and location. Genetic and physical interaction annotation is also supported. Canto captures all necessary information about each interaction for submission to BioGRID. Canto currently supports annotation export in JSON format, either by individual paper or in bulk. The JSON data from Canto can be loaded into a relational database using the Chado schema (as at PomBase) or alternative schemas. +, Curate GO annotations for S. pombe +|
|DIYA +||DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline framework, written in Perl, used for the rapid annotation of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence. === Status === Active development of DIYA is currently on hiatus, pending the hiring of additional people to work on it. [[User:Stewarta|Andrew Stewart]], one of DIYA's developers also has plans to convert the DIYA modules into a series of [[Galaxy]] modules. +|
|GBrowse +||GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include: * Simultaneous bird's eye and detailed views of the genome. * Scroll, zoom, center. * Use a variety of [[GBrowse Configuration HOWTO#Glyphs and Glyph Options|premade glyphs]] or create your own. * Attach arbitrary URLs to any annotation. * Order and appearance of tracks are customizable by administrator and end-user. * Search by annotation ID, name, or comment. * Supports third party annotation using [[GFF]] formats. * Settings persist across sessions. * DNA and [[GFF]] dumps. * Connectivity to different databases, including [[BioSQL]] and [[Chado]]. * Multi-language support. * Third-party feature loading. * Customizable [[GBrowse Plugins|plug-in]] architecture (e.g. run [[wp:BLAST|BLAST]], dump & import many formats, find oligonucleotides, [[PrimerDesigner.pm|design primers]], create restriction maps, edit features) Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used. +|
|GBrowse syn +||GBrowse_syn, or the Generic Synteny Browser, is a [[GBrowse]]-based [[synteny]] browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or co-linearity data from other sources against genome annotations provided by GBrowse. GBrowse_syn is included with the standard GBrowse package (version 1.69 and later). +|
|GO Graphic Viewer +||The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the result from the GO::TermFinder Perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process. This distribution also includes two examples of its use in web browser-based user interfaces (goView.pl and goTermFinder.pl). +|
|GO::TermFinder +||GO TermFinder takes a list of genes as input, and determines whether there are enriched GO terms for that list. These modules provide an object oriented set of libraries for dealing with files produced by the [http://www.geneontology.org/ Gene Ontology project]. In particular, the GO TermFinder object allows a client program to provide a list of genes, from which it will determine p-values for the annotation associated with that list of genes. It does this using the hypergeometric distribution. In addition, a corrected p-value is calculated, to correct for multiple hypothesis testing. This distribution also contains a version of Shuai Weng's GO-View module (and associated classes), such that you can graphically display the output of the GO TermFinder. Some simple clients of these modules are provided in the examples directory of the download. +|
|Galaxy +||A fully-fledged, fully-supported instance +, Test instance +, [http://usegalaxy.org Galaxy] is an open, web-based platform for ''accessible, reproducible, and transparent'' computational biomedical research. * ''Accessibility:'' Galaxy enables users without programming experience to easily specify parameters and run tools and workflows. * ''Reproducibility:'' Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis. * ''Transparency:'' Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis. Galaxy is open source for all organizations. The [http://usegalaxy.org public Galaxy server] makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by [http://getgalaxy.org downloading the Galaxy application] and customizing it to meet particular needs. [[File:GCC2016Logo.png|left|250px|link=https://gcc2016.iu.edu/|2016 Galaxy Community Conference]] === 2016 Galaxy Community Conference === The [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference (GCC2016)] will be held June 25-29, at [https://gcc2016.iu.edu/location/ Indiana University] in Bloomington, Indiana, United states, immediately before the [[Jun 2016 GMOD Meeting|June 2016 GMOD Meeting]], also in Bloomington. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes [https://gcc2016.iu.edu/training two days of training] offering in-depth topic coverage across several concurrent sessions, and [https://gcc2016.iu.edu/hacks/ two days of hackathons]. +|
|InterMine +||InterMine should always be checked out in source code form +, InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the Sequence Ontology and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an XML format to help import custom data. Currently supported formats include Chado, GFF3, FASTA, GO and gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl, UniProt, and many others. A web application allows creation of custom queries, includes template queries (web forms to run 'canned' queries) and can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded. +|
|MAKER +||online version of the MAKER tool +, The ant genomes were annotated using MAKER. +, MAKER is an easy-to-configure, portable genome [[:Category:Annotation|annotation]] pipeline. MAKER allows smaller ''eukaryotic'' genome projects and ''prokaryotic'' genome projects to annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ''ab initio'' gene predictions and automatically synthesizes these data into gene annotations with evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. Its outputs are in [[GFF3]] or [[Glossary#FASTA|FASTA]] format, and can be directly loaded into [[Chado]], [[GBrowse]], [[JBrowse]], [[WebApollo]] or [[Apollo]]. For those annotating novel plant genomes, the [http://www.yandell-lab.org/software/maker-p.html MAKER-P pipeline] is designed to make the annotation tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes. The [http://www.yandell-lab.org/software/maker-p.html MAKER-P website] has more information on the additional protocols for plant genome annotation. Additional MAKER options and capabilities include: * Map old annotation sets on to new assemblies. * Merge multiple legacy annotation sets into a consensus set of annotations. * Update existing annotations to take new evidence into account. * Tag pre-existing gene models with evidence alignments and quality control metrics to assist in downstream manual curation. * Use GFF3 pass-through to include both evidence alignments and predicted gene models from algorithms not natively supported by MAKER. * MAKER is <abbr title="message-passing interface">MPI</abbr>-capable for rapid parallelization across computer clusters. * You can also easily integrate raw InterProScan results into MAKER, which will identify protein domains; add GO functional categories; and help assign putative gene functions to genome annotations. This data then becomes accessible as part of the GFF3 output and can be loaded into a [[Chado]] database, [[JBrowse]], [[GBrowse]], [[WebApollo]] or [[Apollo]]. MAKER comes with sample data for testing purposes. See the <tt>/data</tt> directory in the download. +, …|
|Pathway Tools +||list of PGDBs hosted elsewhere +, Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology: *Development of organism-specific databases called Pathway/Genome Databases (PGDBs) that integrate many bioinformatics datatypes, from genomes to pathways to regulatory networks. *Development of metabolic-flux models using flux-balance analysis *Scientific visualization, web publishing, and dissemination of those organism-specific databases, including: **Automatic display of metabolic pathways and full metabolic networks; generation of metabolic map diagram and of metabolic map poster ([http://bioinformatics.ai.sri.com/posters/ecoli-metab.pdf example]). **Genome browser; comparative genome browser; generation of genome poster ([http://bioinformatics.ai.sri.com/posters/ecoli-genome.pdf example]). **Display of operons, regulons, and full transcriptional regulatory networks *Analysis of omics datasets, including painting omics data on to diagrams of the full metabolic network, enrichment analysis. *Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, prediction of operons *Comparative analyses of model-organism databases. *Analysis of biological networks: **Interactively tracing metabolites through the metabolic network **Finding dead-end metabolites in metabolic networks **Identifying choke points (potential drug targets) in metabolic networks Pathway Tools has four components: *PathoLogic: Creates a new PGDB containing the predicted metabolic pathways of an organism, given a Genbank entry as input. *Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs. The Navigator powers the BioCyc web site at BioCyc.org. *MetaFlux: Supports development of metabolic flux models from Pathway/Genome Databases. *Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs. +|
|Textpresso +||Textpresso is an information extracting and processing (text mining) package for biological literature whose capabilities go far beyond that of a simple keyword search engine. The two key elements are the collection of the full text of scientific articles split into individual sentences, and the implementation of semantic categories, for which a database of articles and individual sentences can be searched. The source of the full text articles are PDFs, and additional bibliographical information that is obtained from other citation databases can be processed as well. [http://ilex.caltech.edu/trac/alere/ Alere] is a package of scripts that can be used to construct a corpus (retrieve articles) for use with '''Textpresso'''. Textpresso is supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health # HG004090. +|
|Tripal +||Tripal is a web front end for [[Chado]] databases, based on the [http://www.drupal.org Drupal] content management system. Tripal leverages many of the features of Drupal--ability to search and edit content, detail pages for different types of content, customizable page layouts, and so on--to provide users with an intuitive, flexible interface to a database. Features and advantages of Tripal: * Allows rapid development of an online genomic database. * Site administrators can add non-biological content to their sites and allow editing of content by non-technical users. * Integrates directly with GMOD [[Chado]]. * Provides visualizations for Chado "modules" such as [[Chado Sequence Module|features]], [[Chado Companalysis Module|analyses]], [[Chado Library Module|libraries]], [[Chado Stock Module|stocks]], [[Chado Modules|and others]]. * Provides an interface for easy editing/updating of data in Chado. * Provides full text and categorical search capabilities for Chado content. * Can integrate GMOD tools such as [[CMap]] and [[GBrowse]]. * Integrates with powerful Drupal features like [http://drupal.org/project/views Drupal views] and [http://drupal.org/project/panels panels] * Provides fully customizable PHP-based templates to allow users to change the look and feel of their installation * Web-based management of Chado (i.e. installation of Chado v1.11 and loading of ontologies) * Loaders for GFF3 and FASTA format files. * Provides an API to allow for creation of custom extensions by anyone. What is Tripal capable of? Check out the [http://tripal.gmod.oicr.on.ca/1.1/ Tripal demo server]. ==== Tripal Homepage ==== Get the most up-to-date information about Tripal [http://www.tripal.info here]. +|
|WebApollo +||WebApollo is a browser-based tool for visualization and editing of sequence annotations. It is designed for distributed community annotation efforts, where numerous people may be working on the same sequences in geographically different locations; real-time updating keeps all users in sync during the editing process. The features of WebApollo include: *History tracking, including browsing of an annotation's edit history and full undo/redo functions *Real time updating: edits in one client are instantly pushed to all other clients *Convenient management of user login, authentication, and edit permissions *Two-stage curation process: edit within a temporary workspace, then publish to a curated database *Ability to add comments, either chosen from a pre-defined set of comments or as freeform text. *Ability to add dbxrefs [database crossreferences] -- e.g. for GO functional annotation *Can set start of translation for a transcript or let server determine automatically *Flagging of non-canonical splice sites in curated annotations *Edge matching to selected feature: matching edges across annotations and evidence tracks are highlighted *Option to color transcript CDS by reading frame *Loading of data directly from GFF3, BigWig, and BAM files, both remotely and from user's local machine. *Configurable heat map rendering of BigWig data *Per-session track configuration to set annotation colors, height, and other properties *Export of annotation tracks as GFF3 and optionally other formats *Search by sequence residues using server-side interface to BLAT or other sequence search programs The public demo can be accessed at: [http://genomearchitect.org/WebApolloDemo http://genomearchitect.org/WebApolloDemo] (''Apis mellifera'' genome). +|
|WebApollo2 +||WebApollo2 is a browser-based tool for visualization and editing of sequence annotations. It is designed for distributed community annotation efforts, where numerous people may be working on the same sequences in geographically different locations; real-time updating keeps all users in sync during the editing process. The features of WebApollo include: *History tracking, including browsing of an annotation's edit history and full undo/redo functions *Real time updating: edits in one client are instantly pushed to all other clients *Convenient management of user login, authentication, and edit permissions *Two-stage curation process: edit within a temporary workspace, then publish to a curated database *Ability to add comments, either chosen from a pre-defined set of comments or as freeform text. *Ability to add dbxrefs [database crossreferences] -- e.g. for GO functional annotation *Can set start of translation for a transcript or let server determine automatically *Flagging of non-canonical splice sites in curated annotations *Edge matching to selected feature: matching edges across annotations and evidence tracks are highlighted *Option to color transcript CDS by reading frame *Loading of data directly from GFF3, BigWig, and BAM files, both remotely and from user's local machine. *Configurable heat map rendering of BigWig data *Per-session track configuration to set annotation colors, height, and other properties *Export of annotation tracks as GFF3 and optionally other formats *Search by sequence residues using server-side interface to BLAT or other sequence search programs The public demo can be accessed at: [http://genomearchitect.org/WebApolloDemo http://genomearchitect.org/WebApolloDemo] (''Apis mellifera'' genome). +, Username: email@example.com, Password: demo +|
|WebGBrowse +||The [[GBrowse|Generic Genome Browser (GBrowse)]] is one of the most widely used visualization tools for sequence display characterized by a rich set of utilities helpful in presenting a variety of genome features pertaining to a reference sequence. Despite the tool being meant for easy use by the biologists, the administration of GBrowse can become tedious, particularly for those without adequate computational resources. Moreover, there is no exhaustive, accurate, "GBrowse user's perspective" based reference available for the various glyphs useful in building the feature tracks on GBrowse, thus adding to the complexities involved in configuration. WebGBrowse guides the users through the process of configuring the [[GFF3]] datasets for GBrowse display. It presents the user with a "Glyph Library" comprising of around 40 different glyphs to choose from. It generates the configuration data by collecting the user's input through an organized, step-by-step process guided by the configurable parameter information available in the glyph library. A summary information on all the available glyphs can be viewed at the glyph library page. A pre-installed GBrowse instance allows the users to preview/load their datasets with desired configuration in GBrowse without requiring them to prepare any computer hardware, install any software or learn sophisticated GBrowse configuration rules for feature display. In other words, WebGBrowse addresses most of the intricacies involved in GBrowse administration, so that even a computer non-savvy biologist can configure his GFF dataset without worrying about GBrowse software installation or GBrowse configuration semantics. WebGBrowse can be [http://webgbrowse.cgb.indiana.edu/software.html downloaded] and installed locally, or you can use the [http://webgbrowse.cgb.indiana.edu/ public WebGBrowse server at CGB]. +|
|XORT +||XORT is a utility written in Perl that can be used to read to and write from a [[Glossary#Relational|relational]] [[Glossary#Schema|schema]] using [[Glossary#XML|XML]] as an interchange format. In GMOD XORT is frequently used to transfer data to and from [[Chado]]. XORT’s three major elements are an XML-database schema mapping specification, an XORT language for both data retrieval and data construction, and a collection of tools that are based on the specification to facilitate the mapping and data exchange. The mapping specification specifies the schema requirement, mapping, operation, and object reference mechanism; the XORT language is used to construct the dump specification; the tool collections comprise the data validation, data input, data output and data debug system. Because it originates from the [[Chado]] database, we denote the corresponding XML "Chado XML." +|