FAQ

Frequently Asked Questions

Locations

Computational Biology Core
Main Location:
Engineering and Sciences Building (ESB), Rm. 206D
181 Auditorium Road, Unit 3214
Storrs, CT 06269
Satellite Location:
400 Farmington Avenue
Farmington, CT 06030

 


Center for Genome Innovation
Main Location:
Engineering and Sciences Building (ESB), Rm. 306A
181 Auditorium Road, Unit 3214
Storrs, CT 06269
Satellite Location:
400 Farmington Avenue
Farmington, CT 06030-6403

HOURS: 9:30am - 5:00pm

1. What are the costs associated with the use of the facilities?

Computational Biology Core:
Use of the CBC's HPC facility (accounts, software, hardware, and server storage) are available free of charge to affiliates of the University of Connecticut.  For analytical services for data related to RNA-Seq, ChiP-Seq, Genome Assembly, and much more - please see our offerings and their related rates available on the this page.  To initiate a project with the CBC, please submit a request here.

Center for Genome Innovation:

A full list of services will be posted to the Fee-for-Services page can be found here. If you have questions or would like more information about any of the services provided by the CGI, contact Bo Reese. 

  • ABI 3130 Capillary Sequencer
  • BioRad CFX 96 Real-Time System
  • Illumina MiSeq
  • Illumina NextSeq 500
  • Affymetrix Gene Chip
  • Affymetrix Gene Atlas
  • Fluidigm C1 Single-Cell Auto Prep, BioMark HD and Access Array systems

Instruments that do not require usage fees for access include:

  • Agilent Bioanalyzer
  • Agilent Tapestation
  • BioRad Experion
  • NanoDrop
  • Hydroshear

2. How should the facilities be acknowledged in resulting manuscripts and grant applications?

Computational Biology Core and Center for Genome Innovation:

Researchers are required to acknowledge the Computational Biology Core, Institute for Systems Genomics, University of Connecticut AND/OR Center for Genome Innovation, Institute for Systems Genomics, University of Connecticut in all publications and grant applications that are enabled by the facilities' resources and services, or include contributions by the facility members.  Please include the facility scientists and/or staff as co-authors when they provide a significant intellectual contribution to the published research. 

Please follow these guidelines for determining authorship:

phd031305s

3. Do you have text that I can use for the facilities portion of my grant proposal?

Computational Biology Core and Center for Genome Innovation: 

The following text can be used in proposals to describe the current facilities and staff members.

4. How do I request a letter of support?

You can request a letter of support from one or both (including the Proteomics & Metabolomics Core) from the following form.  Please place this request at least three days before the due date of the grant application.

5. What type of data storage is available to users?

Computational Biology Core: 

The CBC provides archival (redundant) storage for the Xanadu cluster.  Please note that all temp and scratch spaces on these systems are not redundant (backed up).  Data must be housed in archival portions (/linuxshare) to be archived.  Despite this redundancy, data integrity is the responsibility of the user.  The researcher should ensure an additional copy of critical data is maintained offsite.  

Center for Genome Innovation:

Upon completion of any experiment where data is generated, users must return to the CGI with an external hard drive (or comparable) to retrieve data. If preferred, user data will be made available to them through a secure FTP site. Data will be uploaded to the FTP site by CGI staff and users will be notified when their files are available for download. Files will be kept on the FTP site for 2 weeks, after which the data will be deleted. Prior to deletion, the user will be contacted by CGI staff to ensure that they have downloaded their data and checked to make sure the files are not corrupt, etc.

Data generated by the Affymetrix GeneAtlas or the GeneChip will not be backed up by the CGI. NextGen Sequencing data (raw data files) will be backed up by the CGI for a period of 1 year (or until the allocated backup storage space is full). After 1 year, the user will be notified that data will be removed from the CGI server. Data will not be deleted until the user has been notified and agrees to permanent deletion.

In the case of data generated by the NextSeq 500, all user runs will be created and managed through BaseSpace (Illumina cloud storage). Runs will be initiated through CGI accounts belonging to either Lu Li or Bo Reese. Upon completion of the sequencing run, the ownership (which includes access to run performance metrics reports as well as sequencing data) will be transferred over to the user. Transferring ownership is only possible if the user has an active BaseSpace account. Therefore, prior to beginning a project that will require multiple sequencing runs, the user should create a BaseSpace account. Note that it is not a requirement that users create a BaseSpace account to use the NextSeq 500. If users do not have a BaseSpace account, they must return to the CGI with an external hard drive to collect their data.


Center for Computational Biology Only

1. Can I get CBC support from the UCHC?

Yes, please use the contact-us form or request a project quote to setup an appointment to meet.  Dr. Vijender Singh is onsite at UCHC (Cell and Genome Sciences) on most Tuesdays to meet with people in person there.  

2. I have a class that I would like to teach, can I use the cluster for this?

Currently, we offer the BBC cluster for courses and workshops.  Before you begin the workshop, please send an e-mail to cbcsupport@uconn.edu to provide us with the name of course, when it will be offered, and the approximate number of students enrolled.  We will provide an account page for your course and a dedicated queue on the server (course.q)

3. Which server should I request an account from for research purposes?

Server accounts on Xanadu should be requested for new research.  You will receive a separate form after completing this form from the UCHC HPC team.  After approval of both, you will be able to access the system.  

4. Where can I find information on the teaching (BBC) or research (Xanadu) cluster?

Detailed guides for both clusters are available on our Tutorials page:

BBC Information

Xanadu Information

5. What bioinformatic support resources are available to me?

The CBC offers bi-weekly data therapy sessions in ESB 304 at 10:30am Fridays.  These sessions to everyone and the topic of focus changes each time.  We also have a Slack group (uconn-cbc.slack.com) that provides a forum for users to ask us and other core users questions about software or analysis.  This channel is open to anyone with a UCHC or UCONN e-mail address.  We also curate a list of local workshops, conferences, as well as courses right here on campus through our education page.  We also host several tutorials for common informatic workflows here.  All UCONN affiliates are welcome to setup a consultation with a member of the CBC at anytime.  To request an appointment, please do so here.

Center for Genome Innovation-Specific

1. When is the Center for Genome Innovation open?

Bo Reese and Lu Li have offices in the main laboratory (ESB) of the CGI, with either one or both of them present in the Center between 9:30am and 5:00pm. 

2. Can anyone use the instrumentation in the CGI?

With the appropriate training, anyone can use the instrumentation in the CGI. Depending on the instrumentation, the extent of training can range from a brief, one-on-one informal session to a three day workshop with other individuals. For example, training on the Agilent Bioanalyzer can be done in a one-on-one informal session, while usage of all NextGen sequencing instrumentation requires participation in a three day workshop or a one-on-one individual training.  Even after training, users can request supervision if they are not comfortable working independently.

3. How do I reserve time to use the instruments in the CGI?

All equipment in the CGI is accompanied by a Google Calendar sign-up sheet. You can check the reservation schedule online by contacting either Bo Reese or Lu Li for access to the Google Calendars. Due to high usage volume of most of the equipment, we ask that individuals adhere to the schedules and cancel any reservations if they are no longer needed.

4. How do I determine which Next Generation Sequencing platform is best for my experimental needs?

Most applications are supported by all NextGen sequencing platforms, like whole transcriptome RNA-Seq for example. Having your choice of which platform to use is great because each of the NextGen platforms has a unique way of presenting the data. Although there are certain experimental questions that heavily favor using one platform over another, there are others where the choice is not as clear. For many researchers, the choice in platform comes down to three main factors: genome target, desired genome coverage and cost. The information provided in the table below compares the most frequently used NextGen platforms based on these three (and other) factors.

NGS_May2014

Because the details of each experiment are very different, we encourage you to reach out to us so that we can prepare a budget and sequencing coverage analysis for your experiment. Please contact Bo Reese with your questions.