Araport Project Overview Leaflet (published Aug 6, 2015).

1. Araport is a free online community resource for
Arabidopsis and plant research, funded by the
NSF (US) and BBSRC (UK) since 2013. Conceived
from a community whitepaper [1], Araport
integrates a wide range of data types from
globally distributed and financially independent
data centers into a "one-stop” data shop [2, 3].
Araport is designed to grow with the science
community by providing an extensible framework
to incorporate new data sources and create of
user interfaces to consume them. Find out more
at https://www.araport.org.
Araport has taken on the responsibility of
updating the Arabidopsis genome annotation. In
our latest Araport11 data release, Col-0 gene
structures were validated and updated using 113
RNA-seq data sets along with annotation
contributions from NCBI, MAKER, UniProt, and
individual labs. A pre-release version is available
on the Araport JBrowse and the FTP site. Find out
more at https://www.araport.org/data/araport11.
ThaleMine, an instance of the InterMine
biological data warehouse, serves as our central
data repository. Araport currently hosts genome
annotation which is integrated with data from
UniProt (proteins), NCBI (publications and gene
reference into functions), KEGG (pathways),
ATTED (co-expression), BioAnalytic Resource (BAR,
array expression and interactions), EPIC-CoGe
(epigenomics), Phytomine (plant ortholgs) and
others. Arabidopsis germplasm stocks, genotype,
and phenotype data are expected to be
available in fall 2015. ThaleMine can be used to
search genes, gene functions, biological
processes, pathways, and publications. Find out
more at https://apps.araport.org/thalemine.
Araport uses innovative middleware based on
the iPlant Agave platform to support enrollment,
discovery, and access to community-developed
web services. For example, ThaleMine Gene
Report pages retrieve via web services in real
time co-expression data from the ATTED project,
Japan, and gene expression pictographs from
the BAR project, Canada.
ATTED
BAR
Araport has instantiated a JBrowse genome
viewer which houses the Araport11 data release
including updated gene models, RNA-seq profiles
representing 11 tissues, transcript isoforms, and
other gene evidence. Additional data tracks
include large-scale datasets such as 1001
genome variants (real-time from Ensembl),
epigenomics (real-time from EPIC-CoGe), TDNA-
seq (NCBI/Ecker lab), TAIR10 gene models, and
over 70 additional tracks. Find out more at
https://apps.araport.org/jbrowse.
Araport hosts Science Apps that integrate data
from other web sites using the web services
model of on-request data exchange. These
science apps are developed and published to
Araport by the science community and the
Araport team. Below is a demonstration Science
App which retrieves protein-protein interaction
data from EBI in real-time.
The Arabidopsis Information Portal
Araport11 Genome Annotation
ThaleMine Data Warehouse
Data Federation in ThaleMine
JBrowse Genome Viewer
Science Apps

2. Another example of a Science App displays
KEGG pathway data obtained at run time by
web services. Find out more at
https://www.araport.org/apps.
Araport is an open source science resource and
maintains an active GitHub repository. The
community is not only invited to contribute and
expand functionalities, but is also empowered to
do so. Araport developers exploit cutting edge
technologies such as iPlant, Agave, Adama, git,
jQuery, Bootstrap, Docker, and Swagger. Araport
hosts developer workshops, and hack-a-thons to
help the community enrich and exploit this
resource. Find out more at
https://www.araport.org/devzone.
Summer internships are available for high school
and college undergraduate students who have
interests in biology and computer programming,
and also for teachers interested in developing
curriculum to teach biological subjects using
bioinformatics tools. Find out more at
https://www.araport.org/araport-internship-
program.
[1] International Arabidopsis Informatics Consortium. (2012).
Taking the next step: building an Arabidopsis information portal.
The Plant Cell, 24(6), 2248-2256. PMID: 22751211
[2] Krishnakumar, V., Hanlon, M. R., Contrino, S., Ferlanti, E. S.,
Karamycheva, S., Kim, M., Rosen, B. D., Cheng, C., Moreira, W.,
Mock, S. A., Stubbs, J., Sullivan, J. M., Krampis, K., Miller, J. R.,
Micklem, G., Vaughn, M. & Town, C. D. (2014). Araport: the
Arabidopsis Information Portal. Nucl. Acids Res., 43(D1), D1003-
D1009. PMID: 25414324
[3] Hanlon, M. R., Vaughn, M., Mock, S., Dooley, R., Moreira, W.,
Stubbs, J., Town, C., Miller, J., Krishnakumar, V., Ferlanti, E., and
Pence, E. (2015). Araport: an application platform for data
discovery. Concurrency Computat.: Pract. Exper., doi:
10.1002/cpe.3542.
J. Craig Venter Institute, US
Chris Town [lead]
Jason Miller
Agnes Chan
Texas Advanced Computing
Center, US
Matt Vaughn
University of Cambridge, UK Gos Micklem
Araport is currently seeking “ideas” for
bioinformatics tools (Science Apps) most
needed by the plant community.
You are invited to submit ideas for
bioinformatics tools (Science Apps) that
make use of one or more public data
sources and/or existing tools. The target
user could be either a bench scientist or
bioinformatician.
Submitter of the best idea will receive an
iPad. Find out more at
https://www.araport.org/araportChalleng2015.
Powered by
Funded by
Developer Zone
Internships at Araport
References
Participating Groups and PIs
Ideas Challenge 2015
Win an iPad
Win an iPad
https://www.araport.org
Email: araport@jcvi.org
Twitter: @araport
org
Last modified: Aug 6, 2015