Frequently Asked Questions

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Welcome to Araport! Check out the FAQs to get started. You can also ask a question by visiting the community page. If there's something that's keeping you from doing the work, please drop us a line at araport@jcvi.org

About Araport

The Arabidopsis Information Portal is an open-access online community resource for Arabidopsis research. Araport aims to offer a single interface that allows users to access a wide range of Arabidopsis information. Araport is expandable and will grow through the contributions of research community in the form of data, computation, and visualization tools. You can read more on the About Araport page.

Araport presents data from published literature, including gene and protein expression, gene ontology (GO), interaction, methylation etc. These functions are embedded in ThaleMine or JBrowse.

You don't need one for using search tools and list analysis. However, if you want to save the results for future analysis or share your lists with other users, please create an Araport account.

Unfortunately not. Please create an Araport account.

We'll be posting a public road map of our expected functionality in late 2014.

We have tested the portal (to varying degrees) on recent versions of Chrome, Firefox, and Safari on desktop and mobile platforms. Because we are developing using standardized web toolkits, the majority of the site should work on any reasonable browser. If you find any show stoppers, please feel free to let us know.

We welcome links to Araport.

To access a gene report page
http://www.araport.org/locus/$AGI_LOCUS
http://www.araport.org/locus/At4g25530 (example)

To access a genome browser centered on a locus
http://www.araport.org/locus/$AGI_LOCUS/browse
http://www.araport.org/locus/At4g25530/browse (example)

To access a free-text search of all Araport services
https://www.araport.org/find/$TERM
https://www.araport.org/find/FWA (example)
https://www.araport.org/find/GO:0007275 (example)
https://www.araport.org/find/Soppe%20WJ (example)

To access the Arabidopsis Information Portal site
https://www.araport.org/

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Questions?
Just write to araport@jcvi.org for help.

Araport will provide rich documentation and support to help the Arabidopsis community create its own vision of this portal. For now, if you're interested in working with us, contact us at araport@jcvi.org. We'll set up a conference call and discuss how we might move forward.

Araport is the web site of the Arabidopsis Information Portal project. Araport is maintained by scientists at the J. Craig Venter Institute (JCVI), the Texas Advanced Computing Center (TACC) at University of Texas Austin, Cambridge System Biology Centre (CSBC), and other collaborators. Araport is supported by grants from the National Science Foundation (NSF) in the USA and the BBSRC in the UK. The Araport web site intended to foster scientific research and science education.

Yes, you can post jobs on Araport and it is free of charge. Please register, log in, visit the job page, and click on the "post a job" button.

Alternatively, we could also post it for you if you prefer. Please send the details about the position or a flyer with the information to araport@jcvi.org

Staff at Araport would be happy to post a ad for you. Please send us the title, URL (if available), date, and a brief description of the event. We will promptly post it to the 'Conferences and Meetings' board.

About ThaleMine

ThaleMine is a web app designed to help you explore the Arabidopsis genome. ThaleMine simultaneously accesses and presents multiple data types following a keyword search or a sophisticated queries. The users can view, analyze, share, and explort the results.

Thale indicates thale cress or thaliana, the name given by Linnaeus to honor the plant's discoverer, Johannes Thal. Mine indicates the ‎InterMine technology that enables the integration of complexed biological databases.

ThaleMine integrates public data from a variety of sources including TAIR, BAR, Panther, and GO. The data from TAIR was downloaded en mass, re-organized, and indexed using the data warehouse style of integration. In other cases, i.e. BAR, the data remains distributed across the internet and is downloaded piecemeal at display time using the data federation, or web services, style of integration. The Araport organizers welcome offers or suggestions of new data types and new data sources.

The HTML5 content of ThaleMine requires a fairly recent version of a modern browser such as Chrome 33, Firefox 28, Safari 6, or Internet Explorer 10. There are known minor display issues with FireFox 28 (see the InterMine source code bug tracker 583). ThaleMine is incompatible with Internet Explorer 8 and older versions of MSIE.

ThaleMine links to publications from each protein page and (coming soon) from each gene page. Each list of publications is specific to one protein or gene. The lists were generated by TAIR using NCBI PubMed IDs.

ThaleMine links to orthologs of a handful of model organisms using Mine. The ortholog lists were generated by Panther.

Using ThaleMine

Enter the gene ID in the search box. In the Gene Report page you will find the integration of multiple datasets including gene models, eFP browser, physical and (coming soon) genetic interactions, publication etc.

Enter the keyword in the search box. Filter the search results by gene in the left column. Select the hits (or select all) then click 'create list' tab.

Once you upload the list, the GO term enrichment is one of the default widgets you will see in the report page.

Use this template, and choose the constraint to be your list of interest. In the report table find the column called "Ontology Term Name". Click the "column summary" icon (looks like a histogram) and click "save" in the dialog box. That will download all the GO terms and the numbers of genes belong to each term.

Log in, go to the view page, select the lists of interest, and perform the operation (union, intersect, subtract, or asymmetric difference).

Go to Region, select 'gene'. Enter the genomic regions of this locus (for example: Chr1:29733..37349) and choose 5 kb. You can download the output directly, or create a list for further list analysis

You could use this query and enter your AGI ID of interest as the constraint to extract the associated Curator Summary. To retrieve results for all AGI IDs, you can use the search term 'AT*' as the constraint. You may also further enforce that the constraint be a member of a saved list.

Download InterMine from the Google Play Store and start searching for your favorite gene (e.g. FT, ABI3)

Get it on Google Play

Araport offers several ways to get the up to 3kbp upstream from the transcription start site.

  1. Araport -> ThaleMine -> Templates -> Gene-to-FlankingRegion
    The form lets you ask for the 1kb or 3kp upstream of an AGI. The template query form takes an AGI, an amount of flanking sequence, whether upstream or downstream, and the option to leave out the gene sequence. The results come back as a ThaleMine table from which you can use the “export” button to get a file.

  2. Araport -> ThaleMine -> Home
    Search for your AGI and click on the gene report page (example).
    Scroll down to Genomes / Overlapping Features. Click on “Gene Flanking Regions”. In the table that appears, click on “Fasta” in the row for 3bp upstream. This sends FASTA to the browser. ThaleMine pre-computes flanking regions based on the longest transcript, including UTR, for that locus.

  3. Araport -> Science Apps -> Get-Seqeuence App
    You can install this app in one of your workspaces or just preview it using the Araport main menu -> Tools -> App Store -> Preview this app.
    This has tabs for “search by identifier” or “search by location”. Both let you add up to 4kb of flanking sequence. This app will always include the gene sequence and the upstream and downstream flanking sequence.

  4. Araport -> Web Services -> API Explorer -> get_sequence
    The science app above uses two web services that you could call directly from inside a program. These are called get_sequence_by_coordinate and get_sequence_by_identifier. Each web service has documentation and “try it out” buttons within the API Explorer. Use the /search endpoint for each API.

About JBrowse

JBrowse is a genome browser that allows users to visualize genomes and their features in a customizable form. Users can add or remove the pre-existing tracks. Users can also add a new track to visualize their own (for example, RNAseq) data.

The main difference lies in the rendering strategy: JBrowse is client-side rendering while GBrowse is server-side rendering.

JBrowse does not (yet) offer all the display features of GBrowse2. However, Araport intends to increase the number of tracks in JBrowse over time.

Using JBrowse

Each track displays a certain type of feature. The current tracks in JBrowse include gene models, T-DNA insertion sites, alternative splicing variants, methylation, etc.

Yes. The 'RNA-Seq Based Splice Junctions', 'Alternative Splicing Variants' and three other tracks in EPIC-CoGE facet serve this purpose.

Yes. In JBrowse, click 'file' from the top menu bar and 'open'. Open the BAM and indexed BAM files through uploads or URLs. A new track will then display your RNAseq data. This tutorial video will guide you step-by-step and provide example files for you to get started.

In JBrowse, click 'file' and 'Add sequence search track'. Enter the DNA or amino acid sequence and select the criteria. A new track will show where the motifs present.

There are 2123 non-Arabidopsis plant species in the reviewed Swiss-Prot fasta file (201503) downloaded from UniProtKB. A complete list of species and the number the instances can be found here.

The iPlant Data Store (iDS), made available as part of the iPlant Collaborative Cyberinfrastructure initiative, provides researchers with reliable access to secure cloud-based storage allowing users to offload hosting of large data files (free storage allocation starts at 100GB).

One of the strengths of the iDS infrastructure is providing users with the ability to stream files from the remote location into a variety of Genome Browser applications (like JBrowse, Ensembl, IGV, UCSC) for on-the-fly visualization, supporting the following file formats which represent data such as:

  • read alignments (in SAM/BAM format);
  • variants (in VCF format); and
  • feature annotations (in GFF format)

At Araport, we utilize a JBrowse powered visualization engine to represent different datasets along the Arabidopsis thaliana Col-0 reference genome, some hosted locally and some federated from remote sources like EPIC-CoGe.

In order to view your personal files located on the iDS within the Araport JBrowse, follow the steps outlined below to obtain file sharing link(s):

  1. If not done already, create an iPlant account here: https://user.iplantcollaborative.org.
  2. If not done already, upload your files to the iPlant Data Store using the methods described in the document: Storing and Accessing Your Data in the Data Store. The command-line or iDrop interface is suitable for high-throughput access to storage, while the user-friendly GUI based interface powered by the iPlant Discovery Environment (DE) is more suited for small batch operations.
  3. Visit the DE interface and via the Data Panel, navigate to the location of your dataset(s), formatted as BAM, VCF or GFF.
  4. Use the checkbox adjacent to a file to select the one to send to a remote JBrowse.
  5. In the Details panel, verify the Info-Type attribute for the chosen file and make sure it matches with the file format.
  6. In the Send to: row of the Details panel, click on Genome Browser.
  7. In the resultant popup dialog, you will see an anonymous access URL to the chosen file. Copy this URL to your clipboard.

The above instructions are derived from the iPlant wiki page: Viewing Genome Files in a Genome Browser.

Once sharing links have been obtained, visit the Araport JBrowse and follow the steps outlined below to view the data:

  1. Within the context of the JBrowse interface, click on the File menu in the header and select Open.
  2. In the resultant popup dialog titled Open Files, paste the URLs of the data into the text box titled Remote URLs - one per line (located in the upper-right corner).
    For BAM format files, the supporting BAM index file (BAI) should also be located in the same folder on the iDS. For example:
    BAM file: http://vision.iplantcollaborative.org/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam
    BAM index file: http://vision.iplantcollaborative.org/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam.bai
  3. Once JBrowse recognizes valid URLs, the Files and URLs panel (located in the middle) will be updated, and simultaneously the New tracks panel (located at the bottom) updates with a new track entry showing an auto-populated track label, track glyph type and controls for advanced configuration.
  4. You can repeat the above steps multiple times to add one or more files of interest.
  5. Once all files have been staged, either choose Open Immediately to see the data promptly after clicking the Open button or choose Add to tracks to populate the track selector on the left hand side of the JBrowse window with a list of remotely loaded resources (it will appear at the top of the list, under the category named Local tracks).

Please note: Any tracks loaded using the method described above are only available in that session. When the browser window is refreshed or a new instance/session is opened up in an alternate window/tab, the original set of remote tracks will not be carried over.