From Data to Discovery... 2015 - PAG XXIII Schedule Of Events

The iPlant Collaborative is where scientists in all domains of life sciences (plants, animals, microbes) can connect to public datasets, manage and store their own data and experiments, access high-performance computing, and share results with colleagues. Scroll down to see the events we have planned this year and how you can benefit. If you are new to iPlant, take a tour!

Saturday, January 10th

Workshop Description

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), analyze DNA barcodes and construct phylogenetic trees (Blue Line), and analyze RNA-Seq datasets (Green 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.

Organizer: Dave Micklos - DNA Learning Center/ iPlant

Speakers

Workshop Description

With over 23,000 genomes from 17,000 different organisms, CoGe is where most people are managing and analyzing their genomic data. This two hour workshop will provide in-depth, hands-on training: Managing your genome in CoGe: How to add your own genome to CoGe, add structural and functional annotations, keep it private, share it with collaborators, and make it fully public (http://genomevolution.org/r/8kzz) Integrating functional and diversity data: The EPIC-CoGe addition enables researchers to integrate RNASeq, BS-Seq, ChIP-Seq, DNA resequencing data, microarrays, and any other type of quantitative genomic measurements to any genome in CoGe (http://genomevolution.org/wiki/index.php/EPIC-CoGe_Tutorial) Map NGS reads to a genome: EPIC-CoGe’s RNASeq processing and SNP discovery pipelines make it easy to transform you read data into quantitative measurements. (https://www.youtube.com/watch?v=3fNyHGB02dM) Visualizing your genomic data: The EPIC-CoGe genome browser, based on JBrowse, is instantly available for any genome and associated data loaded into CoGe (http://genomevolution.org/r/9xjy) Whole genome comparisons: Identify and classify orthologous and paralogous genes, identify whole genome duplications, use synteny to order and orient contigs and scaffolds against any reference genome to create pseudo-assemblies Micro-synteny analyses: Identify gene model errors, conserved non-coding sequences, tandem gene duplications, and changes in local genome structure Multiple whole genome synteny analyses: Given a gene in one genome, find syntenic regions across multiple genomes, even if that specific gene is not present. CoGe offers a multitude of advanced on-the-fly analyses. To accomplish these, CoGe is part of the Powered by iPlant Program and leverages iPlant’s Cyberinfrastructure for computational scalability. Learn more about this program at: http://www.iplantcollaborative.org/discover/powered-by-iplant

Organizer: Eric Lyons

Co-chairs: Eric Lyons and Haibao Tang

Speakers

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Come as you are to this informal demo and Q&A session to see the latest features from 3 popular cyberinfrastructure resources.  We will cover a variety of tools and datasets that help beginning and expert users tackle the bioinformatics and data challenges associated with genome assembly, annotation and RNA-Seq. Researchers working with microbes, plants, and animals can leverage these freely available resources. If you are an existing user, this is also a chance for you to give us feedback on what you like most, and what you’d like to see more of. Stop by for a few minutes, or stay for the entire presentation and cover hands-on tutorials that will get you started analyzing and visualizing data right away.

• iPlant – Comprehensive cyberinfrastructure for all life sciences, data management, cloud resources, and more.
• KBase – The DOE Knowledge base; integrated analyses across plants, microbes, and their communities.
• Gramene - Curated, open-source resource for comparative functional genomics in crops and model plant species

Sunday, January 11th

iPlant Booth (Open from 3:00PM - 8:30PM)

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Technological advances have changed the way biologists conduct research – now take advantage of these new technologies to prepare students to succeed as the scientists of the future. With the advent of high-throughput technologies in data-generation as well as in computing, faculty are challenged to find ways to prepare their students to succeed in an environment which changes at a seemingly ever-increasing pace. Come and join fellow educators in an informal setting to find out how to include high-throughput technology in your teaching.

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The ability to amass data is outpacing the ability of researchers to effectively collaborate and to transform these acquired data sets into high-value results in a timely manner. Managing the lifecycle of research data at this rapidly growing scale necessitates interdisciplinary collaborations and team science approaches, often spanning multiple teams, departments and institutions. This discussion will focus on the effective use of cloud based infrastructures for managing data and computation for research teams. We will demonstrate methods and discuss best practices from various groups making use of iPlant cyberinfrastructure and NSF XSEDE to manage their data intensive workflows.

Monday, January 12th

iPlant Booth (Open from 9:30AM - 5:00PM)

Workshop Description

This workshop is for biologists who are working with large data sets. It will feature talks, tutorials, and demos that will help you use free, NSF-funded resources (#DBI-1265383) for a variety of data-intensive analyses (e.g. genome assembly and annotation, RNA-Seq, image analysis, GWAS, geospatial etc.). Users with limited bioinformatics experience, or experienced users who need access to greater HPC capacity will both benefit from attending. Whether you’re just getting started with high-throughput sequencing, or have been working with biological big data for years - data analysis and management are usually the most challenging aspects of investigation. Some challenges are obvious up front (“my files are too large to share”); some challenges appear later on (“I can’t replicate because metadata is missing or my previous software has disappeared”) – working with cyberinfrastructure can help solve these challenges and more. In this workshop we’ll cover the platforms, tools, and services developed by the iPlant Collaborative and demonstrate how research communities studying arthropods, microbes, animals are using them. The workshop is targeted at anyone working with large datasets and will • Overview of available resources (data storage/sharing, web interfaces, cloud computing) • “Get started” demos on tools, platforms, and intro to RNA-Seq analysis • Presentations by researchers who have used used these tools to solve problems • How tool developers can make their tools and pipelines more accessible to the research community For more information on related presentations and hand-on bioinformatics and developer tutorials at this year’s PAG, please visit www.iplantc.org/pag2015

Organizer: Jason Williams - Cold Spring Harbor Laboratory / iPlant

Speakers

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Calling all bioinformaticians and bioinformatics enthusiasts! We're hosting a small get together on a variety of topics relevant to making bioinformatics accessible and open to all communities. If you have ever contributed code to an open source project, helped with documentation, or trained students and colleagues we'd like to invite you down to this late-night event. Our goal is to gather feedback on how we can all leverage cyberinfrastructure investments and support open source bioinformatics that works for every investigator and student. We will talk about projects such as Data Carpentry (http://datacarpentry.org/) and how you can get involved. Please RSVP and submit discussion topics at: www.iplantc.org/freeicecream

Tuesday, January 13th

iPlant Booth (Open from 9:30AM - 3:00PM)

Speaker: Nirav Merchant, University of Arizona / iPlant

This computer demonstration will show you how to use Atmosphere, iPlant's cloud compute platform, for creating, sharing, and publishing virtual appliances (machine images) for reproducible analysis.

Atmosphere allows you to easily configure and bundle complex bioinformatics applications and their underlying software dependencies, in a ready-to-use form. It supports applications with GUI (Graphical User Interface) and web interfaces; end users can access Atmosphere and the virtual appliances using a web browser to launch their analysis.

Learn to use Atmosphere as a gateway to access iPlant's core infrastructure resources, including high performance computing (HPC) environments and the iPlant Data Store. We will demonstrate how you can extend this environment using Docker-based containers and how to add more applications to an existing virtual appliance.  We will also build an appliance during the demo, from start to finish, and share it with attendees.

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Managing data and metadata can pose a significant barrier to effective scientific investigation, collaboration, and publication.  This workshop will focus on existing resources and tools to allow Life Sciences researchers to overcome these barriers, and exciting platforms on the horizon to move from data and metadata organization to the management of entire projects.  The tools presented will accommodates a broad range of skill levels, with web-based and command line access to your data, the efficient transfer of large datasets, and metadata association and searching.

Visit our Booth (#231)

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.

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Related workshops, presentations, and posters

See the work of our friends, colleagues, and collaborators. Is your presentation/poster missing? Email info@iplantcollaborative.org

Social Media

Stay in touch with us throughout the event!

Twitter: @iPlantCollab #iPlantPAG

Facebook: facebook.com/iPlantCollab

LinkedIn: iplant.co/iPlantCollabLinkedIn

Google+: iplant.co/iPlantGooglePlus

iPlant is funded by the National Science Foundation (#DBI - 1265383)