Data Therapy 

These sessions will be held bi-weekly on Fridays.  
We welcome beginners and advanced users to generate a productive discussion! 
To get an idea of the group size (and your general interests) - we have a very quick survey
This survey will also form an independent mailing list for this event so fill this out if you want to keep updated on our meetings!

CBC Events

Data Therapy Week – 12 : RNA-Seq Challenges

Friday, July 14th at 10:00 am at BioPharm 203 - Storrs CT

 

Data Therapy Week – 11 : Introduction to Xanadu HPC (Storrs)

Friday, June 30th at 10:00 am at BioPharm 203 - Storrs CT

- Introduction to the Xanadu Cluster 

CBC_DataTherapy_HPC_Xanadu_introduction (Download  .ppt)

 

Data Therapy Week – 10 : Metatranscriptomics

Friday, June 16th at 10:00 am at BioPharm 203 - Storrs CT

- Focus of Metatranscriptomics:

- Common RNA Seq techniques 

- Challengers 

- Typical Analytical Pipeline

- Read or Transcript Processing

- Visualizing Results

 CBC_DataTherapy_Week10_Metatranscriptomics 

Data Therapy Week – 09 : HPC Basics and Introduction to Xanadu Cluster

Friday, June 2nd at 10:00 am in R1401 Cell and Genome Science Building - Farmington, CT

- Introduction to High Performance Computing 

- A Typical HPC cluster

- Connecting to Xanadu Cluster 

- Common Linux Commands

- Software on the Cluster and How to Access

- Composing a (SLURM) Script for Xanadu Cluster

CBC_DataTherapy_HPC_Xanadu_Introduction_Week09

 

Data Therapy Week – 08 : Metagenomics

Friday, May 19th at 10:00 am in BioPharm 203.

- General workflow

- Resources ( 16S / Genomes / Metagenomes / Function )

- General Challenges / Considerations

- Marker Genes

- Bioinformatics workflow 

CBC_DataTherapy_Metagenomics_Week08 

Data Therapy Week – 07 : RNA-Seq

Friday, May 5th at 10:00 am in BioPharm 203.

- RNA-Seq versus Microarrays

- RNA-Seq workflow

- Designing the Study

- Paired versus Single-End

- Analysis Challenges

- One Gene: Two Isoforms: Opposite Functions

- Quality Control

- Read Mapping or Assembly

- Generating Raw Reads

- Differential Expression

CBC_DataTherapy_RNASeq_Week07

Data Therapy Week – 06 : Introduction to HPC Resources

Friday, April 21st at 10:00 am in BioPharm 203.

- BBC cluster and it's different nodes

How to open a graphical terminal to display (pdf and image files)

- In the cluster working directory (or in Home directory), using a terminal type: python -m SimpleHTTPServer
- In a new terminal using your PC/lap-top run: ssh -NL 8000:localhost:8000 <user_name>@bbcsrv3.biotech.uconn.edu  , and leave the terminal window open.
- Then open a browser window in your computer and type: http://localhost:8000 to view your working directory and to open pdf and image files.

- How to submit a single job and a array job using qsub

- Data transfering

Data Therapy Week – 05 : ChIP-Seq

Friday, April 7th at 10:00 am in BioPharm 203.

DataTherapy_ChipSeq_Week05

Data Therapy Week – 04 : RADSeq

Friday, March 24th at 10:00 am in BioPharm 203.

DataTherapy_Week04

Data Therapy Week – 03 : Genome Assembly

Friday March 3rd at 10.00 am in BioPharm 203
Discussed ideal sequencing strategies for de-novo genome assembly of  Non-model species.

Discussed genome assembly tools/softwares e.g.: MaSuRCA, Allpaths, SOAPdenovo2, SPAdes

What type of sequencing data is better when you are doing a population studies?

How to go about doing assembly when you have RAD-seq data.

CBC Open House 2017

Friday, 24th of February at  Grossman Auditorium, Cell and Genome Science Building, UConn Health Center.  [schedule]

Data Therapy Week – 02 : Discussion on Databases

 Friday, Feb. 17th at 10:00am in BioPharm 203.

Data Therapy Week – 01 : Introduction to the CBC and the resources

Feb 3rd 2017
DataTherapy_Week01

Next Session

July 14th 2017 

RNA-Seq Challenges

Friday, July 14th at 10:00 am at BioPharm 203

Storrs CT

Online Support

Connect to the CBC team through #bioinformatics_help channel at
uconn-cbc.slack.com