PAG XXII

Saturday: DNA-Subway Workshop (10:30AM - California Room: Session 2135)

Date: Saturday, January 11th, 2014

Time: 10:30 AM - 12:40 PM

Location: California Room

Session Abstract: This workshop introduces DNA Subway (dnasubway.iplantcollaborative.org), an educational bioinformatics platform developed by the NSF-sponsored iPlant Collaborative. DNA Subway bundles research-grade bioinformatics tools and databases into intuitive workflows - presenting them in an appealing interface modeled on the metaphor of a subway map. “Riding” on different DNA Subway lines, students can predict and annotate genes in up to 150 kb of DNA (Red Line), identify homologs in sequenced genomes (Yellow Line), and analyze DNA barcodes and construct phylogenetic trees (Blue Line). With support for plant and animal genomes, DNA Subway engages students in their own learning by bringing to life key concepts of gene structure and function, genome organization and complexity, and evolutionary biology. An integrated experiment on DNA Barcoding illustrates the modern synthesis of in vitro biochemistry with in silico bioinformatics, and provides an opportunity to merge molecular genetics with ecology and conservation biology. Presenters from a variety of undergraduate institutions will show how they are using DNA Subway to support novel, course-based and independent student research. Participants will also preview forthcoming improvements to DNA Subway. A new Green Line analyzes RNA-Seq datasets using high performance compute resources of NSF’s Extreme Scientific and Engineering Discovery Environment (XSEDE). Upgrades to the Red Line will provide a simple-to-use annotation and browser system, which seamlessly integrates data from local RNA-Seq experiments. This will create a “power desktop” that allows students to explore large-scale variation in gene expression and genome structure on their personal computers.

PAG Abstract Link: http://pag14.mapyourshow.com/5_0/sessions/sessiondetails.cfm?ScheduledSessionID=1DA8

Sunday-Tuesday: iPlant Booth (227)

Come meet with members of the iPlant team! This is our chance to get to meet our users, reconnect with people who have been to our workshops. See demos of iPlant tools and services and get your questions answered.

Sunday, Monday: iPlant Mini-workshop on Genome assembly, annotation and RNA-Seq (Stratford Room)

NEW: Workshop WIKI link

This workshop will cover hands-on examples to get you started doing Genome Assembly, Annotation, and RNA-Seq using tools developed by iPlant:

• Discovery Environment: Simple web portal for managing data, analyses, and workflows. Complex bioinformatics applications can be run without knowing command line programming; users can also integrate their own tools.
• Data Store: Scalable, secure, and reliable storage for terabyte-scale data.
• Atmosphere: One-click, on-demand cloud computing.

Our examples will cover assembly with ALLPATHS, annotation with MAKER, and RNA-Seq with the Tuxedo Suit of tools.

Who Should Attend? Any investigator (PIs, post-docs, grad students, industry users) who is or will be working with large datasets and computation-intensive research questions in the life sciences (plants and animals!).

Registration: There is NO registration, but Seating is limited and not guaranteed. Come as you are and if there is a seat stay a while! We will also be on hand to answer any and all other questions related to iPlant.

What should I bring: If you wish to follow any demos, you may wish to bring a Wi-Fi enabled laptop.

* Both workshops will cover the same materials

 

Sunday: CartograTree Demo (Stratford Room)

Successfully identifying the genes and specific alleles associated with traits of interest in forest trees is dependent on the ability to access genotype, phenotype, and environmental data. The future of these association studies lies in next-generation sequence data, ontologically sound phenotypes, and geo-referenced measures.  Cartogratree leverages modern web technologies to interact with the Google Maps API on the front-end and web services, including SSWAP (Simple Semantic Web Architecture and Protocol), to connect to data points on the back-end.  CartograTree serves genomic and phenotype data from the TreeGenes database, phenotypes from the TRY-DB resource, and environmental data from Ameriflux and WorldClim. Combined, these resources amount to over 10,000 trees, 90,000 phenotypes, and 10 million genotypes. Along with the user’s ability to upload custom data in the form of phenotype or environmental measures, data mutability is supported by allowing the sub-setting and merging of sets of tree samples based on their phylogenies, previous studies, or geographical location. Custom parameterization (e.g. removing missing data) is also supported.  The user interface allows both simple and complex searches, and can be initiated based on functional information, sequence identifiers, tree identifiers, and related criteria. The cornerstone feature is the integration of the iPlant Cyberinfrastructure’s SSWAP to connect the user to all of the available data around a given tree and to software that can perform association analysis, such as TASSEL. Explore Cartogratree at: http://dendrome.ucdavis.edu/cartogratree

Monday: iPlant Birds of a Feather (BoF) Meeting on Analysis Pipelines, Clouds, HPC & API (Stratford Room)

The meeting will start with a brief overview of upcoming capabilities at iPlant to support high throughput pipelines using DE, Atmosphere and Agave API, followed by an open discussion. Our main goal is to get feedback from iPlant users, so we hope this will be a highly interactive discussion. It is not necessary to RSVP for this event, but if possible, we would appreciate you letting us know whether or not you will attend by emailing nirav@iplantcollaborative.org.

Tuesday: Main iPlant Workshop Unified Cyberinfrastructure for All Life Sciences (10:30AM - California Room: Session 2171)

Date: Tuesday, January 14

Time: 10:30 AM - 12:40 PM

Location: California Room

Abstract:
This workshop showcases the free data storage, computation, and bioinformatics tools, developed by the iPlant Collaborative - an NSF-funded cyberinfrastructure project (#DBI-0735191) (renewal grant #DBI-1265383). iPlant's services life science researchers and educators working in all domains of life, enabling them to understand and make increasingly powerful predictions about biological systems. iPlant's mission includes empowering discovery at multiple levels, from making bioinformatics applications accessible to the “average bench-biologist” to enabling big-data science that would not otherwise be possible. This workshop features a variety of presentations by investigators who have used iPlant cyberinfrastructure to aid their research and demonstrates how you can leverage these free resources for a variety of genomics related analyses (e.g. genome assembly and annotation, RNA-Seq, re-sequencing, etc.), as well as other bioinformatics applications. In the first 5 years, iPlant successfully developed a platform of integrated technologies and computational resources that provide access to large data storage, high-performance computing, grid computing, and cloud computing. These resources are made available to scientists by providing access at multiple levels including application programming interfaces (APIs), RESTful services, and web-based systems for data access, tool integration, and analysis. We will discuss how the next 5 years of development will expand the capabilities of our “genotype-to-phenotype” science enablement plan, and how community input will shape our continued support for data-driven biologists. Register for your free iPlant account at user.iplantcollaborative.org. Please also visit our booth and training sessions that will be advertised here: www.iplantc.org/pagxxii

Invited Speakers:

PAG Abstract Link: http://pag14.mapyourshow.com/5_0/sessions/sessiondetails.cfm?ScheduledSessionID=1EAE

Tuesday: iPlant Semantic Web Platform SSWAP: Simple Semantic Web Architecture and Protocol (1:30PM - Towne: Session 2172)

Date: Tuesday, January 14

Time: 1:30 PM - 3:40 PM

Location: Towne

Abstract: The iPlant Collaborative Semantic Web Platform uses SSWAP (Simple Semantic Web Architecture and Protocol) as the underlying technology for dynamic, semantically-aware pipelines. Scientists or any user can make pipelines by dragging-and-dropping services in a Web-based Rich Internet Application. On the backend, an automated transaction-time description-logic reasoner is continually examining the pipeline as it is being constructed so that those services and only those services that satisfy the data semantics are offered at any given step. Web sites can also semantically tag their data, and users can launch into pipelines with that data to discover those services that can operate on the data. We demonstrate how this novel Web integration links TreeGenes' CartograTree with iPlant's High Performance Computing resources via one-click semantic discovery. SSWAP Web Discovery enables Web sites to discover and engage a distributed suite of services as scientific pipelines, thus enabling a scientific, semantic Web infrastructure. Third-party developers may publish their own services which are then automatically available for semantic discovery and pipelines. This workshop introduces users and developers to iPlant's Semantic Web Platform. Topics include an introduction to the vision of the program, its technologies, a guest application, and how to use it as both a scientist and a developer. The web site is at http://sswap.info.  

Invited/Potential Speakers:

PAG Abstract Link: http://pag14.mapyourshow.com/5_0/sessions/sessiondetails.cfm?ScheduledSessionID=1EA1

Tuesday: iPlant Birds of a Feather (BoF) Meeting on Metadata, Standards, and Ontologies (Stratford Room)

The meeting will start with a brief presentation of the new and in progress metadata and search capabilities at iPlant, followed by an open discussion. Our main goal is to get feedback from iPlant users, so we hope this will be a highly interactive discussion. iPlant's initial focus has been on metadata capabilities and standards for genomic data from large genome resequencing or transcriptomic projects, but our infrastructure metadata capabilities can be used for almost any type of data. It is not necessary to RSVP for this event, but if possible, we would appreciate you letting us know whether or not you will attend by emailing rwalls_at_iplantcollaborative.org.

Slides: Metadata_in_iPlant_Jan2014

iPlant-related Posters/Presentations @ PAG

Social Media

Twitter: @iPlantCollab #iPlantPAG

Facebook: facebook.com/iPlantCollab

LinkedIn: iplant.co/iPlantCollabLinkedIn

Google+: iplant.co/iPlantGooglePlus