Author: Perera, Neranjan

UCONN Health VPC Discontinued

Posted on January 14, 2020 by Perera, Neranjan

VPC (vpc.cam.uchc.edu) will be discontinued February 1^st, 2020.

GENEIOUS PRIME

For Geneious Prime users, please see our Tutorials page on how to download and install Geneious Prime for your local computer:

Tutorials

* Please note, you must be connected to the CAM VPN for Geneious

Data Therapy(Friday, December 20th @ 10:30am) Data compression

Posted on December 10, 2019 by Perera, Neranjan

Friday, Dec 20th at 10:30 am in ESB 304. Xanadu cluster : Data Compression

Join for a basic discussion on Xanadu cluster and bring your questions !!!

Want to join us remotely, follow the link http://s.uconn.edu/esb304webex

We have put together a schedule of events with short training sessions including a wide range of tips and tricks to improve your interaction with HPC and data analysis! We will have sessions on cluster usage, data compression/transfer, R, differential expression, and more! Check out the schedule below and plan to join us bi-weekly on Fridays at 10:30am in ESB (shiny new building!, between Chemistry and PBB), room 304. The next session is on December 20th on running Data compression. Don’t want to leave your office? You can join us via the web conference given above.

Schedule for Data therapy sessions: https://bioinformatics.uconn.edu/data-therapy-schedule/

Data Therapy(Friday, December 6th @ 10:30am) Resource request

Posted on December 5, 2019December 5, 2019 by Perera, Neranjan

Friday, Dec 6th at 10:30 am in ESB 304. Xanadu cluster : Resource request

Join for a basic discussion on Xanadu cluster and bring your questions !!!

Want to join us remotely, follow the link http://s.uconn.edu/esb304webex

We have put together a schedule of events with short training sessions including a wide range of tips and tricks to improve your interaction with HPC and data analysis! We will have sessions on cluster usage, data compression/transfer, R, differential expression, and more! Check out the schedule below and plan to join us bi-weekly on Fridays at 10:30am in ESB (shiny new building!, between Chemistry and PBB), room 304. The next session is on Dec 20th on running Data compression. Don’t want to leave your office? You can join us via the web conference given above.

Schedule for Data therapy sessions: https://bioinformatics.uconn.edu/data-therapy-schedule/

Data Therapy(Friday, November 22nd @ 10:30am) Interactive Sessions

Posted on November 18, 2019 by Perera, Neranjan

Friday, Nov 22nd at 10:30 am in ESB 304. Xanadu cluster : Interactive sessions

Join for a basic discussion on Xanadu cluster and bring your questions !!!

Want to join us remotely, follow the link http://s.uconn.edu/esb304webex

We have put together a schedule of events with short training sessions including a wide range of tips and tricks to improve your interaction with HPC and data analysis! We will have sessions on cluster usage, data compression/transfer, R, differential expression, and more! Check out the schedule below and plan to join us bi-weekly on Fridays at 10:30am in ESB (shiny new building!, between Chemistry and PBB), room 304. The next session is on Dec 6th on running Resource request on Xanadu. Don’t want to leave your office? You can join us via the web conference given above.

Schedule for Data therapy sessions: https://bioinformatics.uconn.edu/data-therapy-schedule/

Data Therapy(Friday, November 8th @ 10:30am) Xanadu introduction

Posted on November 7, 2019November 7, 2019 by Perera, Neranjan

CBC Data Therapy Details!

Friday, October 25th at 10:30 am in ESB 304. Xanadu cluster : Basic Introduction

Want to join us remotely, follow the link http://s.uconn.edu/esb304webex

Please join us with your questions!

We welcome beginners and advanced users to generate a productive discussion!

To get an idea of additional interests and needs – we have a very quick survey. Our sessions are offered bi-weekly so join us again on 11th October

Looking forward to your questions and issues.

Data Therapy(Friday, October 25th @ 10:30am) General consultation

Posted on October 24, 2019November 7, 2019 by Perera, Neranjan

CBC Data Therapy Details!

Friday, October 25th at 10:30 am in ESB 304. General Consultation

Want to join us remotely, follow the link http://s.uconn.edu/esb304webex

Please join us with your questions!

We welcome beginners and advanced users to generate a productive discussion!

To get an idea of additional interests and needs – we have a very quick survey. Our sessions are offered bi-weekly so join us again on 11th October

Looking forward to your questions and issues.

Tips and Tricks for Illumina RNA-Seq Applications – Seminar

Posted on October 15, 2019October 15, 2019 by Perera, Neranjan

CGI will be hosting a RNA-Seq library preparation and sequencing seminar:

Learn about various RNA-Seq library preparation and sequencing applications and then meet with Illumina Specialists for one-on-one consultations during our Office Hours.

Speaker: Michael Smith Ph.D. (Illumina, Inc.)

Location: Engineering and Science Building

Room 121

67 North Eagleville Road

Storrs, CT 06269

Date: October 16, 2019

Time: 10am – 12pm

For more information, or to RSVP for this event please email Bo Reese (bo.reese@uconn.edu)

Data Therapy(Friday, October 11th @ 10:30am) General consultation

Posted on October 10, 2019October 10, 2019 by Perera, Neranjan

CBC Data Therapy Details!

Friday, October 11th at 10:30 am in ESB 304. General Consultation

Want to join us remotely, follow the link http://s.uconn.edu/esb304webex

Please join us with your questions!

We welcome beginners and advanced users to generate a productive discussion!

To get an idea of additional interests and needs – we have a very quick survey. Our sessions are offered bi-weekly so join us again on 11th October

Looking forward to your questions and issues.

Data Therapy(Friday, September 27th @ 10:30am) General consultation

Posted on September 26, 2019October 10, 2019 by Perera, Neranjan

CBC Data Therapy Details!

Friday, September 27th at 10:30 am in ESB 304. General Consultation

Want to join us remotely, follow the link http://s.uconn.edu/esb304webex

Please join us with your questions!

We welcome beginners and advanced users to generate a productive discussion!

To get an idea of additional interests and needs – we have a very quick survey. Our sessions are offered bi-weekly so join us again on 11th October

Looking forward to your questions and issues.

Upcoming workshops

Posted on August 19, 2019September 10, 2019 by Perera, Neranjan

CBC Workshops are open to advanced undergraduates, graduate students, postdocs, and faculty. Each class enrolls a maximum of 12 students and provides hands-on training and background for genomics data analysis. Two instructors are available to assist participants as they work through the provided exercises. All materials, including sample and processed data files, are available after the course ends. Workshops will be offered at the Storrs and UCH campuses. Students are welcome to register and attend workshops at either location. We do not assume or require experience with high performance computing or programming. The listed workshops still have spaces available, including the upcoming variant detection workshop!

To register, please follow this link: https://bioinformatics.uconn.edu/cbc-workshops/

Variant Detection (Location: Storrs) – August 22-23, 2019

HPC Introduction

Experimental design considerations

Read alignment

SNP detection with GATK (GBS)

SNP detection with Freebayes (exome capture)

SNP detection with Samtools

SNP annotation with SNPeff

Pathway Analysis (Location: Storrs) – November 21-22, 2019

Gene Annotation with BLAST2GO/EnTAP

Gene Enrichment Analysis with GOrilla, DAVID, GSEA

Pathway Analysis with Cytoscape

Pathway Analysis with IPA