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Content with tag gateway showcase .

Webinar: Gateway Showcase featuring I-TASSER and Chem Compute

September 13, 2017

Gateway Showcase featuring

I-TASSER
Presented by Chengxin Zhang, Department of Computational Medicine and Bioinformatics, University of Michigan

and

Chem Compute
Presented by Mark Perri, Assistant Professor of Chemistry, Sonoma State University

Details

I-TASSER Science Gateway for Protein Structure and Function Prediction
Chengxin Zhang, S. M. Mortuza, and Yang Zhang
Department of Computational Medicine and Bioinformatics, University of Michigan

Abstract: I-TASSER (Iterative Threading ASSembly Refinement) is a composite method for atomic-level protein structure prediction and structure-based protein function annotation. The on-line server system has been widely used by the biomedical community with registered users coming from more than 130 countries. In Fall 2016, I-TASSER began using XSEDE’s Comet supercomputer; as a result, I-TASSER singlehandedly tripled Comet’s users by adding more than 8,000 unique users in the first several months of integrating with Comet. In this presentation, we will discuss the following: (1) How I-TASSER generates protein structure and function predictions; (2) how I-TASSER is integrated with the XSEDE Gateway system and how the XSEDE resources have enhanced the functionality of I-TASSER and its usefulness to the community; (3) How to use the I-TASSER Gateway and how to interpret the I-TASSER output results for normal users; and (4) how to improve the quality of the I-TASSER model for advanced users (e.g. introduction of restraints, and strategy for modeling multi-domain proteins etc). The I-TASSER gateway is available at http://zhanglab.ccmb.med.umich.edu/I-TASSER/.

Chem Compute Science Gateway:  Computational Chemistry for Undergraduates
Presented by Mark Perri, Assistant Professor of Chemistry, Sonoma State University

Abstract: We report on our efforts to provide a free, easy to use, but powerful interface for undergraduate students to submit computational jobs.  Computational experiments are critical for engaging students in Physical Chemistry because they provide the opportunity for visualization of concepts, such as molecular orbitals.  The Chem Compute Science Gateway allows students to submit jobs to the NSF XSEDE supercomputer network.  Students can submit jobs using the GAMESS (General Atomic and Molecular Electronic Structure System) ab initio quantum chemistry package and the TINKER Molecular Modeling Package (Molecular Dynamics).

Slides about I-TASSER

Slides about Chem Compute

Watch on YouTube


Webinar: Gateway Showcase featuring VectorBase and CitSci.org

June 14, 2017

Gateway Showcase featuring VectorBase and CitSci.org

Watch the YouTube recording

 

VectorBase: A bioinformatics resource for invertebrate vectors and other organisms related with human diseases 
Presented by Gloria I. Giraldo-Calderón, PhD, VectorBase Scientific Liaison/Outreach Manager 
Contact: ggiraldo at nd dot edu

Abstract: VectorBase (www.vectorbase.org) is a free, web-based bioinformatics resource center (BRC) for invertebrate vectors of human pathogens, funded by NIAID/NIH. This database is the ‘home’ of 40 genomes of arthropod vectors and pests and also has transcriptomes, proteomes and population data for an even wider list of species. The population biology data includes lab and field collected information and, in addition to the data imported from external databases or directly submitted by users, VectorBase also generates and computes primary data. Over its 13 years of existence, the discovery and interpretation of hosted data has been used for basic and translational research, as expressed in numerous scientific publications, using data from one or more studies in new or re-purpose analyses, descriptions, and hypotheses testing. Raw and process data can be exported or downloaded in a variety of different formats, visualized, browsed, queried and analyzed with the site tools or any other external tools. VectorBase data, tools, and resources are updated every two months. The website has extensive documentation resources for new and experienced users including tutorials, video tutorials, practice exercises, answer keys, and sample files. 

Download the slides as PDF

CitSci.org: A platform for engaging citizen scientists through individualized websites 
Presented by Greg Newman, Director CitSci.org & Research Scientist, Natural Resource Ecology Laboratory, Colorado State University 
Contact: Gregory.Newman at colostate dot edu

Abstract: Citizen science empowers individuals to pursue their interests in the scientific world. Members of CitSci.org are encouraged to investigate their own scientific questions or jump on board as a volunteer for an existing project. In parallel, citizen science programs create their own online projects where trained volunteers and scientists together answer local, regional, and global questions, inform natural resource decisions, advance scientific understanding, and improve environmental education. The platform provides tools to empower the citizen science gateway creators and their participants to ask questions, select methods, submit data, analyze data, and share results. CitSci.org provides tools for the entire research process and full spectrum of citizen science program needs: creating new projects, managing project members, building custom data sheets, analyzing collected data, and gathering participant feedback. To date, our volunteer coordinators have started 414 projects that have contributed a total of 697,984 measurements for analysis to answer local, regional and/or global questions.

Download the slides as PDF


Webinar: Gateway Showcase featuring Ensayo Project's SimEOC and Spatial Portal for Analysis of Climatic Effects on Species (SPACES)

April 12, 2017

Gateway Showcase featuring 

Ensayo Project's SimEOC: A Web-Based Virtual Emergency Operations Center Simulator for Training and Research and 

Spatial Portal for Analysis of Climatic Effects on Species (SPACES) 

Watch the YouTube recording

 

Ensayo Project's SimEOC: A Web-Based Virtual Emergency Operations Center Simulator for Training and Research

Presented by Greg Madey, University of Notre Dame

Abstract: Training is an integral part of disaster preparedness. Practice in dealing with crises improves one’s ability to manage emergency situations. As an emergency escalates, more and more agencies get involved. These agencies require training to learn how to manage the crisis and to work together across jurisdictional boundaries. Consequently, training requires participation from many individuals, consumes a great deal of resources in vendor cost for support and staff time, and cannot be conducted often. Moreover, in the current crisis management environment, most training is conducted through discussion-based tabletop and paper-based scenario performance exercises. SimEOC was developed under the NSF-funded Ensayo Project. It is a web-based training simulator and research tool. SimEOC is built using MongoDB, Express.js, Angular and Node.js (the MEAN stack). A design overview and demonstration will be provided.

Download a PDF of the Ensayo Project's slides

Questions asked about Ensayo Project (answered in the video)

If you want to try out the gateway or have further questions, email gmadey AT nd DOT edu

  • Can anyone get an account for the SimEOC and do the exercises?
  • Please comment on the development process....
  • Who would configure these exercises? How do you add new facilities related to emergency management?
  • When did collaboration with CRC begin? how was the broader development team scoped and organized?
  • Has this system been used in a real training situation?
  • Did CRC have enough visibility at ND that you knew to reach out? Otherwise, how did you learn of them?

Spatial Portal for Analysis of Climatic Effects on Species (SPACES)
Presented by Dilkushi de Alwis Pitts, University of Cambridge

Abstract: To deal with escalating environmental shifts caused by climate change and other factors, ecologists are increasingly called upon to make risk assessment decisions about affected natural resources. As a result, there is a rapidly growing need for niche modeling of species projections to guide management decisions and activities related to intervention.

A number of software applications exist for carrying out fundamental niche modeling, but they present several problems for users, including distinct approaches to algorithms, data, and outputs, among others. The openModeller software was created to address these concerns by providing transparent, open-source tools under a common architecture.

SPACES builds on openModeller to manage for biologists the complication of running niche models, including data formatting and the complexities of the modeled systems. SPACES has endeavored to resolve the issues mentioned above by obtaining, handling, and storing the large quantities of data that niche models require, processing the data in a user-controlled way, and presenting the results in convenient formats. Through SPACES, extensive, quality spatial data are made available alongside species data and a variety of niche models that can be executed, analyzed, and compared—all through a common Web browser interface, designed to support a virtual scientific community and share the results of research.

Questions asked about SPACES Project (answered in the video)

If you want to try out the gateway or have further questions, email kad49 AT cam DOT ac DOT uk

  • Does SPACES use HPC to run jobs? If yes, which one(s)?
  • Are all the output spatial raster data? Otherwise, how to do map algebra on vector data? Where does map algebra happen, in user's browser or a backend server? If latter, how to manage the computation?
  • What does it cost to add a new model algorithm? How much automation has been done to speed it up?
  • How do other researchers put their algorithms into SPACES portal?