News

ISG Computational Biology Core Virtual Workshops – September 2020

The Computational Biology Core within the Institute for Systems Genomics is pleased to announce two virtual workshops in September!

Workshop descriptions and registration links can be found here: https://bioinformatics.uconn.edu/cbc-workshops/

Topic: Virtual Variant Detection Workshop
Date: September 14-17 (4 days)
Time: 9am-12pm
Location: Online
Cost: $300
For anyone with keen interest and desire to develop variant detection analytic skills

Day 1: Introduction to Linux, HPC
Day 2-4: Introduction, Reference genome prep , download data, QC and trimming of data, align and compress, Sort, mark duplicates, index, Understanding SAM files, Freebayes, GATK, Understanding VCF files, hard filters, comparing variant sets, snpEFF annotation, IGV

For anyone with keen interest and desire to develop RNA-Seq analytic skills in systems that do not have a well resolved reference genome.

These workshops are not pre-recorded and at least two instructors are available to assist users as we walk through the tutorials. If you have questions on the content or registration details, please do not hesitate to contact us at cbcsupport@uconn.edu

Server Upgrades in Progress: Limited Xanadu Access

The draining of several nodes in preparation for the Xanadu HPC power upgrade and hardware expansion is moving faster than expected.  As such, we are currently planning to complete the power upgrade on the morning of July 27th (rather than the previously announced August 4th).

To further accommodate job submissions during this time, we have a temporary special queue with a job time limit of 3 days. This can be accessed with qos set to: special and partition set to special in your Slurm script or interactive session.  Please note, if you want to access the himem nodes, you should set partition to special_himem and keep qos set to special

 

 

Upcoming CBC Workshops 2020 (July-August)

The Computational Biology Core within the Institute for Systems Genomics is pleased to announce three virtual workshops for the months of July and August!

Workshop descriptions and registration links can be found here: https://bioinformatics.uconn.edu/cbc-workshops/

 

Topic: Introduction to Linux and HPC
Date: July 6th
Time: 9-12pm
Location: Online
Cost: $50
This workshop is recommended for anyone getting started with the High Performance Computing (HPC)!  This includes background on Linux, working with the Slurm scheduler, and the basics of submitting and monitoring jobs.
Topic: RNA-Seq Analysis (Model)
Dates: July 13th-16th (4 days)
Time: 9am-12pm daily
Location: Online
Cost: $300
This workshop will focus on experimental design, high throughput sequencing basics, quality control, alignment to a reference genome, differential expression analysis, and functional annotation. Tools presented are appropriate for researchers working in systems with a reference genome.
Topic: RNA-Seq Analysis (Non-Model)
Dates: August 3rd-6th (4 days)
Time: 9am-12pm daily
Location: Online
Cost: $300
This workshop will focus on experimental design, high throughput sequencing basics, quality control, de novo transcriptome assembly, differential expression analysis, and functional annotation.  Tools presented are appropriate for researchers working in systems without a reference genome.
These workshops are not pre-recorded and at least two instructors are available to assist users as we walk through the tutorials. If you have questions on the content or registration details, please do not hesitate to contact us at cbcsupport@uconn.edu

Read Aligners

Hello CBC Users!

Please join us for another Data Therapy session this Friday, March 6th at 10:30am in ESB 304.
We’ll be giving an overview of the Read Aligners.
There will also be time to help you with any other problems or questions you may have about the cluster or your data analyses.
If you want to join us remotely, follow this link.

Xanadu Cluster Introduction

Hello CBC Users!

Please join us for another Data Therapy session this Friday, February 7th at 10:30am in ESB 304.
We’ll be giving an introduction to Xanadu cluster and computing resource.
This is a very good introduction for new users.
There will also be time to help you with any other problems or questions you may have about the cluster or your data analyses.
If you want to join us remotely, follow this link.

Data Therapy – Data/File transfer

Hello CBC Users!

Please join us for another Data Therapy session this Friday, January 17th at 10:30am in ESB 304.  This is our first session for 2020.
We’ll be talking about Data/File transfer on Xanadu.
There will also be time to help you with any other problems or questions you may have about the cluster or your data analyses.
If you want to join us remotely, follow this link.