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- Update the gene '''xfile''': change the name symbol to '''x-file''' and retrieve the changed record. Regenerate the report from Problem 1. T symbol: x-file40 KB (5,672 words) - 21:27, 15 August 2013
- ** db=short symbolic name of datasource (MOD), used to look up conf file ** Sequence feature apps should read/write GenBank & EMBL formats (BioPerl and BioJava handle this). GFF? GTF? BED? GAME? BSML? TIGR add BSML6 KB (985 words) - 05:18, 28 January 2008
- File:Cmap_sample1.jpg File:Cmap_sample2.jpg7 KB (996 words) - 23:40, 17 October 2013
- [[File:Flash gviewer title.jpg|center|Flash GViewer Logo]] ...ckwaveFlash&promoid=BIOW here]. To edit the source code (the <tt>.fla</tt> file in [[SVN]]) and publish modified versions of the <tt>.swf</tt> requires Mac2 KB (339 words) - 19:41, 26 February 2014
- * Annotations can come from a static XML file or can be dynamically generated by a server-side script ...cript that retrieves the data from a database. Details of the various file formats are given below.30 KB (4,819 words) - 21:16, 9 October 2012
- * Supports third party annotation using [[GFF]] formats. ...ns|plug-in]] architecture (e.g. run [[wp:BLAST|BLAST]], dump & import many formats, find oligonucleotides, [[PrimerDesigner.pm|design primers]], create restri11 KB (1,422 words) - 16:47, 10 April 2023
- * DNA files (full chromosomes) in raw and fasta formats * Gene Ontology association file10 KB (1,496 words) - 23:00, 15 August 2013
- | install = See the INSTALL file in the [http://sourceforge.net/projects/gmod/files/blastGraphic/ blastGraph | input = <!-- input formats -->1 KB (188 words) - 18:37, 10 September 2013
- ...from other MODs in terms of data models, user interfaces and data exchange formats. As a result, the research community has to struggle to adjust to new user ...s. Compute interoperability allows software to communicate via shared file formats, transport protocols and database schemas. Both types of interoperability a26 KB (3,975 words) - 05:03, 28 January 2008
- ** flexible configuration of data output formats ...eports and instead expect users to parse information from current, defined formats (which can vary wildly between databases). Some MODs (e.g. FlyMine) allow18 KB (2,786 words) - 17:34, 31 January 2008
- * XORT exchanges data between XML file and database. XORT is generic * GenBank flat-file format to chadoXML converter (Peili Zhang, Chris28 KB (4,338 words) - 22:06, 29 October 2010
- ...|database]]. This does not have to be a relational database; it could be a file or a set of files with or without some kind of index. There's a lot of flex ...e application and translates them to database queries, then receives data, formats it, and sends it back to the application. This piece of software can be tho34 KB (5,526 words) - 19:56, 7 October 2013
- .... In our view these two formats are complementary. Conversions between the formats should be trivial. ...library and follow the instructions in the <code>chaos-xml/INSTALL</code> file.4 KB (647 words) - 21:08, 22 January 2008
- formats. ...The basic state is that users parse information from a given MOD's defined formats (which tend to vary between MODs). Some MODs (e.g. FlyMine, FlyBase) allow24 KB (3,905 words) - 16:54, 11 August 2008
- sh: line 1: ./Build: No such file or directory make images (generates images of the schema in several formats)16 KB (2,472 words) - 23:54, 25 January 2008
- ;<nowiki>Bio::SCF File::Temp</nowiki> io-lib(v1.7+) This will give you a .tar.gz file, which must be uncompressed and unpacked. Then run the following commands35 KB (5,565 words) - 22:39, 8 August 2012
- ...e organism-specific webstart build of Apollo and an accompanying ant build file for repeating the build. ** Chado2Wiki worked via dumps to intermediate flatfile formats11 KB (1,683 words) - 19:54, 9 June 2010
- ...omputer parsable data URL, with no guesswork on spelling, and defined data formats. | Returns a FASTA file containing big DNA fragments (e.g. chromosomes). MIME type is application/x4 KB (607 words) - 22:44, 15 September 2009
- ...f hashes: Bio::SeqFeature::Slim. This is 70% faster for reading a [[GFF]] file. Bio::Feature::IO only supports [[GFF3]]. It is slow, uses heavy objects, * Couple XML response to URL request formats.28 KB (4,093 words) - 05:54, 5 January 2011
- ...and analyses. The customers generally have genome data in hand, in common formats of which Fasta (sequence) and [[GFF]] (annotation) are most common. Custom ...LuceGene Lucegene] : Bio-data indexer that understands various genome data formats, now in use for grid data splitting. Lucene/Lucegene are in java. Advantan7 KB (1,032 words) - 22:42, 15 September 2009
- N-Browse version 2 can save/export data in a variety of formats. Please visit [http://www.gnetbrowse.org N-Browse] for more information. === N-Browse Version 1 Source Code Download (tar.gz file) ===6 KB (920 words) - 16:57, 30 September 2010
- [[File:InterMineLogo.png|link=http://www.intermine.org/wiki/NowHiring|180px|right| ...a warehouses of biological data. It can integrate data from many different formats into a central database and makes the data available to query via a flexibl1 KB (188 words) - 23:12, 9 October 2012
- [[File:InterMineLogo.png|link=http://www.biomed.cam.ac.uk/gradschool/skills/interm ...e] for examples. InterMine can integrate data from many common biological formats and is easy to extend to include your own data. Parsers are included to loa2 KB (283 words) - 23:12, 9 October 2012
- ...after the initial hurdles of learning about configuration options and file formats are overcome. This talk is intended to introduce the more advanced features2 KB (301 words) - 19:41, 18 October 2019
- [[File:web_apollo_demo_login_page_with_credentials_2014.jpg|WebApollo login page|c [[File:web_apollo_select_refseq_2014.jpg|WebApollo reference sequence selection|ce77 KB (11,812 words) - 00:39, 21 May 2014
- ...[GFF]]''' is a standard file format for storing genomic features in a text file. GFF stands for '''''G'''eneric '''F'''eature '''F'''ormat''. GFF files a ...to as GFF2.5. GTF is not a supported format in GMOD so if you have a GTF file you'll need to convert it to [[#GFF3|GFF3]].14 KB (2,081 words) - 02:50, 14 March 2014
- <div class="guideline">When uploading a file, please give the file a meaningful '''Destination filename'''.</div> ...n the file is. Therefore the filename should describe the contents of the file.16 KB (2,420 words) - 23:18, 8 November 2013
- [[File:Das_logo_64x64.jpg|right|link=http://www.biodas.org/|Distributed Annotation * Couple XML response to URL request formats.2 KB (224 words) - 18:47, 17 September 2012
- | [http://genome.ucsc.edu/FAQ/FAQformat.html UCSC Formats] | [http://genome.ucsc.edu/FAQ/FAQformat.html UCSC Formats]3 KB (443 words) - 16:22, 7 August 2012
- ; [[CMapDumper.pm]] : Dumps a tab delimited file that can be read by CMap. ; [[ProteinDumper.pm]] : Dumps translated protein sequences in various formats.2 KB (320 words) - 17:00, 4 December 2012
- <br>[[File:Aug2009MeetingPhoto.JPG|August 2009 GMOD Meeting]] | [[File:GMOD2009Europe300.png|link=GMOD Europe 2009|GMOD Europe 2009]]59 KB (8,741 words) - 19:37, 4 September 2013
- ...ata. After loading, access and rendered performace is equal for all three formats. * Some aspects of the data display can be controlled in the wiggle file15 KB (2,251 words) - 21:22, 25 April 2013
- [[File:Aug2009MeetingPhoto.JPG|link=August 2009 GMOD Meeting|right|August 2009 GMO ...Sequence alignment/map format (SAM) and SAMtools|SAM and SAMtools]]: file formats and programs for compact representation of [[Next Generation Sequencing]] d2 KB (301 words) - 19:37, 4 September 2013
- | [[File:Paglogo.gif|link=http://www.intl-pag.org/|PAG 2009]] * download the zip file and double-click to unpack3 KB (431 words) - 19:34, 3 October 2012
- | valign="center" |[[File:SanDiegoConvention.gif|link=http://www.sandiego.org/nav/Visitors|San Diego [[File:Jan2009Meeting.JPG|center|Jan 2009 Meeting]]50 KB (7,612 words) - 18:53, 8 October 2012
- The sample below is in CLUSTALW format. Other formats are also supported (see below). ==Note on formats==7 KB (897 words) - 21:27, 14 August 2012
- '''GFF''' is a standard file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 c Finally, ''[[#GTF|GTF]]'' is another file format that is very similar to GFF and is sometimes referred to as GFF2.5.16 KB (2,336 words) - 19:49, 10 September 2012
- '''GFF''' is a standard file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 c Finally, ''[[#GTF|GTF]]'' is another file format that is very similar to GFF and is sometimes referred to as GFF2.5.16 KB (2,387 words) - 22:13, 11 February 2014
- [http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml GFF2] is a supported format in GMOD, '''but it is now de The GFF file format stands for "Gene Finding Format" or or "General Feature Format" and17 KB (2,719 words) - 13:27, 21 April 2017
- ...ls.sourceforge.net SAMtools], a platform agnostic set of programs and file formats for efficiently storing and retrieving short read data.3 KB (450 words) - 00:52, 18 November 2010
- | [[File:Ba2009.png|450px|link=http://www.ausbiotech2009.com.au/bia/bia-home|Bioinfo : The presentation slides are available in two formats. The PowerPoint contains a few useful animations.4 KB (456 words) - 18:52, 8 October 2012
- [[File:Jbrowse_arch.png|600px]] Starting config file:9 KB (1,327 words) - 22:46, 3 October 2012
- ...after the initial hurdles of learning about configuration options and file formats are overcome. This class is intended to help them over those hurdles. * The Data File2 KB (328 words) - 18:52, 8 October 2012
- [[File:ApolloLogo.png|thumb|180px|[[Apollo]]'s new logo, designed by [[Spring 2010 [[File:RedFlyLogo.png|thumb|150px|[http://redfly.ccr.buffalo.edu/ REDFly's] new lo4 KB (668 words) - 01:33, 15 September 2012
- ...alignment database from a multiple sequence alignment file. A variety of formats are supported, including [http://www.bioperl.org/wiki/FASTA_multiple_alignm ...enome alignments but a number of other applications can emit or read these formats.6 KB (931 words) - 22:39, 21 February 2013
- ===The alignment data file=== ...used to process these data will recognize clustalw and other commonly used formats recognized by BioPerl's [http://search.cpan.org/~birney/bioperl-1.2.3/Bio/A19 KB (2,507 words) - 18:53, 8 October 2012
- | [[File:ABRF2010Header.jpg|center|600px|link=http://www.abrf2010.org/|ABRF 2010]] ...that the browser knows about. Make sure that the first column of your GFF file says NC_003070.917 KB (2,763 words) - 18:52, 8 October 2012
- | rowspan="2" | [[File:GMOD2010Europe300.png|center|220px]] [[File:Sept2010MtgLogo300.png|150px|link=September 2010 GMOD Meeting|September 20110 KB (1,367 words) - 17:04, 2 April 2013
- | rowspan="1" | [[File:Sept2010MtgLogo300.png|250px|center]] ...MOD Meeting</b><br />13-14 September 2010<br />Cambridge, UK <br /><br />[[File:Sept2010Group.jpg|center]]100 KB (14,725 words) - 17:31, 30 November 2012
- There are, as yet, no standard flat file formats or loading scripts to load data into this module. Custom scripts will need30 KB (4,604 words) - 16:35, 30 January 2013
- | rowspan="1" | [[File:Sept2010MtgLogo300.png|220px|link=September 2010 GMOD Meeting|September 201 <div style="font-size: 220%; line-height: 140%">[[File:InterMineLogo.png|link=InterMine|300px|InterMine]]<br /><br />2 KB (338 words) - 18:53, 8 October 2012
- ...e] and on the [https://github.com/GMOD/Apollo/blob/master/README.md README file on GitHub]. *Export of annotation tracks as GFF3 and optionally other formats4 KB (536 words) - 20:37, 6 April 2015
- ...ent the database with their own data as Custom Tracks in a variety of file formats including BAM, SAM, GFF, GFF3, BedLoader, and more. Users can upload data f ...tion is a listing of all the tracks contained within the original uploaded file, along with the options you have to manipulate it, such as deleting it, rem12 KB (2,045 words) - 22:35, 29 December 2010
- Do you know of any other genome assembly formats? I guess AGP is BioPerl supports the following assembly formats:12 KB (1,905 words) - 20:08, 5 April 2011
- [[File:Annotation-workflow.jpg|center|Annotation workflow]] [[File:Architecture.jpg|Apollo architecture|center]]34 KB (5,242 words) - 00:21, 14 February 2013
- | [[File:AGSBug170.png|Arthropod Genomics Symposium||Arthropod Genomics 2011]] *pyu-contig.fasta - a FASTA file containing a 1.7 MB contig15 KB (2,338 words) - 18:52, 8 October 2012
- :'''Get Data → Upload File → ftp://ftp.gmod.org/pub/gmod/Meetings/2011/AGS/3263.maker.output/3263 :: This uploads the GFF file into Galaxy. It recognizes it as a GFF3 file.2 KB (374 words) - 20:04, 9 June 2011
- '''GFF''' is a standard file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 c Finally, ''[[#GTF|GTF]]'' is another file format that is very similar to GFF and is sometimes referred to as GFF2.5.16 KB (2,350 words) - 20:25, 12 July 2016
- ...the JBrowse directory somewhere in the web-servable part of your server's file system (often <code>/var/www</code> by default) ...user pointing their web browser at the appropriate URL for the index.html file in the JBrowse directory will see the JBrowse interface, including sequence185 KB (26,536 words) - 02:48, 30 September 2020
- ...the CMS increases the version level of new updates to an already existing file. Version control is one of the primary advantages of a CMS. ...pal does require command-line access to the web server with adequate local file storage for loading of large data files. Be sure to check with your servic131 KB (21,091 words) - 21:53, 2 January 2014
- ...the CMS increases the version level of new updates to an already existing file. Version control is one of the primary advantages of a CMS. ...pal does require command-line access to the web server with adequate local file storage for loading of large data files. Be sure to check with your servic99 KB (16,007 words) - 17:43, 12 July 2013
- ...ids_from_fasta.pl</tt> in the same directory which will go through a FASTA file and extract all the ids from the deflines. Let’s first create the list o We need to deploy the WAR file in the war directory from the unpacked tarball.55 KB (8,533 words) - 19:02, 24 August 2013
- File:Cmap_sample1.jpg File:Cmap_sample2.jpg6 KB (814 words) - 18:31, 10 September 2013
- '''GFF''' is a standard file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 c Finally, [[#GTF|GTF]] is another file format that is very similar to GFF and is sometimes referred to as GFF2.5.16 KB (2,352 words) - 21:54, 11 September 2012
- * Creates initial configuration files, including the main file <tt>universe_wsgi.ini</tt>, and empty directories for storing data files ...e are many ways to do this, but the simplest is by uploading or fetching a file.32 KB (4,846 words) - 21:16, 9 October 2012
- ...ult, but this location can be configured in the <tt>universe_wsgi.ini</tt> file: ...xist in the previously specified folder. The contents of the <tt>.len</tt> file is tab-delimited and specifies the length of each chrom/contig of that buil16 KB (2,444 words) - 21:16, 9 October 2012
- ...ids_from_fasta.pl</tt> in the same directory which will go through a FASTA file and extract all the ids from the deflines. Let’s first create the list o We need to deploy the WAR file in the war directory from the unpacked tarball.88 KB (13,531 words) - 19:06, 20 March 2017
- ...tureCoverage track type that generates a depth-of-coverage plot from a BAM file (or from any other source of feature data). Many thanks to Thomas Down and ...ng sequence and annotation data in FASTA, GFF3, bed, bedGraph, and Wiggle formats. Just turn on the track of interest and click on its track label to bring8 KB (1,340 words) - 01:13, 6 November 2012
- that generates a depth-of-coverage plot from a BAM file (or from any other source of feature data). Many thanks to Thomas Down and ...ng sequence and annotation data in FASTA, GFF3, bed, bedGraph, and Wiggle formats. Just turn on the track of interest and click on its track label to bring2 KB (393 words) - 01:39, 6 November 2012
- * Supports third party annotation using [[GFF]] formats. ...ns|plug-in]] architecture (e.g. run [[wp:BLAST|BLAST]], dump & import many formats, find oligonucleotides, [[PrimerDesigner.pm|design primers]], create restri8 KB (1,065 words) - 18:35, 10 September 2013
- * [[File:XORTSpecification_0.pdf|XORT Specification]] | formats =4 KB (518 words) - 18:48, 10 September 2013
- | doc = Documentation is provided in the README file in the [http://sourceforge.net/projects/gmod/files/GOView/ GO Graphic Viewe | input = <!-- input formats -->2 KB (293 words) - 18:38, 10 September 2013
- ...our own [[Chado]] instance) to even creating new adapters to read new data formats or schemas. ...that our [[Chado]] connectivity is working. Let's save our work using '''File → Save as...'''.34 KB (5,278 words) - 22:36, 12 February 2013
- ...t>. However, if the file already exists, it will use the already existing file. and save the file.38 KB (5,631 words) - 23:56, 13 February 2013
- '''GFF''' is a standard file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 c Finally, ''[[#GTF|GTF]]'' is another file format that is very similar to GFF and is sometimes referred to as GFF2.5.16 KB (2,345 words) - 00:23, 14 February 2013
- [[File:MineManager-welcome.png]] [[File:MineManager-minesettings-info.png]]43 KB (6,258 words) - 17:56, 14 February 2013
- [[File:TripalLogo.png|250px|right|link=http://www.ncbi.nlm.nih.gov/pubmed/24163125 ..., Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan X2 KB (333 words) - 18:46, 1 November 2013
- ...ids_from_fasta.pl</tt> in the same directory which will go through a FASTA file and extract all the ids from the deflines. Let’s first create the list o We need to deploy the WAR file in the war directory from the unpacked tarball.64 KB (9,974 words) - 18:35, 14 November 2013
- To setup jbrowse on your server, the basic idea is to download the zip file, drop the files in a folder on a web server, and run the setup.sh script. * downloading the zip file from jbrowse.org, e.g. https://jbrowse.org/releases/JBrowse-1.12.1.zip65 KB (10,432 words) - 15:23, 16 September 2020
- data (all subsets of the experiment) in one text file, where... structure of the file in fact is one of the most simple wiggle...61 KB (1,369 words) - 22:29, 6 April 2018
- ...eb application for analyzing [[GFF3]] annotations. [[GFF3]] is a standard file format for genomic annotation data. SOBA gathers statistics from GFF3 file ...ider variety of tables, figures and graphs based on the data in a [[GFF3]] file, as well as the ability to produce complex and extensible custom reports vi19 KB (2,557 words) - 14:38, 19 May 2014
- ...the CMS increases the version level of new updates to an already existing file. Version control is one of the primary advantages of a CMS. ...pal does require command-line access to the web server with adequate local file storage for loading of large data files. Be sure to check with your servic131 KB (21,099 words) - 00:18, 20 February 2014
- ...ids_from_fasta.pl</tt> in the same directory which will go through a FASTA file and extract all the ids from the deflines. Let’s first create the list o We need to deploy the WAR file in the war directory from the unpacked tarball.86 KB (13,281 words) - 00:37, 19 November 2014
- '''GFF''' is a standard file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 c Finally, ''[[#GTF|GTF]]'' is another file format that is very similar to GFF and is sometimes referred to as GFF2.5.16 KB (2,318 words) - 04:56, 19 May 2014
- * To make life easier on you, you can add an entry in your /etc/hosts file for the IP address of the EC2 machine that resolves to tutorialpag30.jbrows * Created a bgzipped and samtools faidx'ed FASTAs file for ''C. elegans'' and ''C. brenneri''.34 KB (5,728 words) - 18:21, 23 January 2023
- == JBrowse 2 Plugins synteny formats== ...is able to visually compare multiple genomes. Adding support for new file formats for that comparison would be valuable. The goal of this project would be to9 KB (1,387 words) - 18:23, 16 March 2023
- ...fe easier on you, you can add an entry in your client machine's /etc/hosts file for the IP address of the EC2 machine that resolves for tutorialpag31.jbrow * Created a bgzipped and samtools faidx'ed FASTAs file for ''C. elegans'' and ''C. brenneri''.39 KB (6,446 words) - 03:36, 18 January 2024
