Skip to content

Latest commit

 

History

History
231 lines (155 loc) · 8.59 KB

other-cyverse-services-faq.rst

File metadata and controls

231 lines (155 loc) · 8.59 KB
Raw

|CyVerse_logo|_

|Home_Icon|_ Learning Center Home

CyVerse Services FAQ

About CyVerse FAQ

Is CyVerse infrastructure open access/open source?

Yes, some of CyVerse is open access. Anyone can access (browse and retrieve) publicly available datasets. However, you must register for an account to upload data and run analyses.

All CyVerse code is open source and can be found on CyVerse GitHub. Read our Open Source Policy.

Data FAQ

Analysis FAQ

What apps and workflows are in CyVerse?

CyVerse has hundreds of apps and workflows in the Discovery Environment (DE). For the list of applications available in the DE, see the List of Applications. Most apps in the DE have user manuals to give you a jump-start on using the app. You also can browse the list of tutorials to find help to learn a complicated workflow or how to use an app in the DE or VICE.

How can I make my app available for other people to use?

You can create a new app interface in the Discovery Environment and share it with other users and you also can install the app on VICE. In most cases, providing a Docker container (or a link to one) with the application of your choice is all you need to start. See the Developer's section of the |CyVerse Learning Center|.

Bring Your Own (BYO) FAQ

How can I use CyVerse's tools and resources from within my program/app?

See the information about our Science APIs; you can also contact Support using the blue chat icon |Intercom| at the bottom right of the platform. For projects requiring more extensive support, you can request community support or an external collaborative partnership (see Collaboration FAQ below).

Collaboration FAQ

How can I get a letter of collaboration for my grant proposal that uses CyVerse?

To request a letter of collaboration, email informaticians@cyverse.org with the following information: - the CyVerse resources your project will use (e.g., storage, computing power, expertise for scaling, etc.) and indicate if any resulting datasets will be made publicly available in CyVerse - the name of the PI, proposal title, funding agency, and date you need the letter - if there is a template that must be used, please attach to your email

What is an external collaborative partnership and how do I apply?

External Collaborative Partnerships (ECP) pair member(s) of the CyVerse user community with expert CyVerse staff to address the computational needs of a scientific project. Requests are reviewed on an ongoing basis.

The criteria CyVerse uses to review ECP requests are available here: |ECP criteria|.

To help you complete the |ECP application|, the questions on the form are listed below.

External Collaborative Partnership Application Questions

See the full list of questions below:

Expand to read more

  • Project Principal Investigator (PI)

  • Institution

  • Collaborating personnel

    • Provide a detailed list of students, technicians, informaticians and/or developers who will be able to assist with project design and implementation, their respective computational science skill sets (e.g., web design, Python, GWAS, etc.), and their specific time commitments during the project (e.g., 1.5 hrs/day).

  • Previous interactions with CyVerse

  • Funding sources

  • Project title

  • Project description

  • Please summarize your proposal’s activities and desired outcomes (500 chars or less)

  • Scientific description

    • Provide a scientific description of your project. Describe how the proposed project is within the scope of CyVerse’s scientific Enablement Vision. Illustrate how any resulting deliverables have the potential to enable science for scientists beyond your immediate network of collaborators.

  • Technical description

    • Provide a technical description of your project. What is the computational need that Will be addressed with assistance from CyVerse? Identify specific potential deliverables to be implemented using CyVerse technologies, such as the Discovery Environment, Atmosphere, APIs, Data Store, Data Commons, etc.

  • Timeline and milestones for completing the project

    • Provide a timeline of specific monthly milestones (deliverables). Projects of short duration (~2 months) should provide weekly milestones.

  • Scientific and technical impact

    • Describe how the success of this collaboration will benefit your project and the broader community.

  • Communication and sharing plan

    • Will the data and/or workflows be made publicly available through CyVerse?
    • Will you be blogging and/or tweeting about the work?
    • Will you be giving a talk about your work at your institution or at a professional conference?
    • Will you be writing a news article for the CyVerse website or newsletter?
    • Will you be preparing a tutorial that uses the datasets or workflows?
    • Will you be leading a workshop(s) or webinar(s) to teach others to use the data or workflow(s)?
    • Describe any other plans to communicate how your project will use CyVerse

Training FAQ

How can I use CyVerse in my course?

DNA Subway (See |DNA Subway Guide|) is especially useful for teaching gene concepts, phylogenetics, DNA barcoding and RNA-Seq. With a friendly user interface and based on the analogy of multiple subway stops and lines, student learn the basics of computational genomics workflows.

Using containers in DE/VICE is also a great teaching resource. By loading a container with the software tools, datasets, and analysis parameters necessary to run an analysis, containers help overcome many technological hurdles for both learning and teaching informatics.

Can CyVerse give a workshop at my institution?

Funding to support workshop requests is very limited, with priority for trainings at underserved institutions (rural, HBCU/Tribal/Hispanic-serving, etc.). Contact Education, Outreach, and Training Lead Jason Williams (williams@cshl.edu)

Fix or improve this documentation

|Home_Icon|_ Learning Center Home