Archive 2017
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CBC Newsletter September 2017

September 2017 - Updates from the ISG Computational Biology Core (CBC)
 
**We've Moved!**  Find our Bioinformatics Scientists in the new ESB Building.  As always, contact us in advance to schedule an appointment.**
 
Group Data Therapy Sessions - Biweekly on Fridays at 11:30am!
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.
 
We will be hosting our next Data Therapy Session to provide an introduction to shell scripting on the Xanadu cluster THIS Friday, September 8th at 11:30am in ESB 205 (new building between Pharmacy and Chemistry).  Please note the new time and location.
 
 
New Server - More Cores!  Welcome to Xanadu!
If you are seeking more resources - memory and cores - obtain a UCH account (CAM) here: http://bioinformatics.uconn.edu/contact-us/ (select UCH)
 
This will provide access to our new cluster Xanadu.  Xanadu utilizes Slurm rather than SGE for job management.  To learn how to access and interact with the Xanadu cluster, please go here:
 
Old Server (BBC users) - Please move your data to Xanadu!
BBC users should be in the process of moving their data over to Xanadu.  Please contact the CBC if you need assistance.  Please clear your home directory AND data residing on /tempdata3 as soon as possible.  The /archive is still available for longterm data storage and will be mounted to Xanadu in the future.

Announcing a mini ChiP-Seq Winter Workshop
CBC Workshops are open to advanced undergraduates, graduate students, postdocs, and faculty.  Each class enrolls a maximum of 10 students and provides hands-on training and background for genomics data analysis.  Use the following survey to tell us about the training you or your group members need.  Registration for the following will open soon!
 
ChIP-Seq: Experimental Design and Analysis
Date: December 18th 2017 (9-1pm)
Location: UCH Campus
Cost: $200
 
Geneious!
The CBC is now hosting five commercial floating licenses for the Geneious software package.  To access these licenses - please follow the instructions posted here:
 
To learn more about Geneious, visit: http://www.geneious.com
 
Need Pathways?  Access Qiagen's IPA is coming soon!
After assessing the needs of the UConn/UCH research community, it was decided that Qiagen's IPA will offer more useful features to meet current analysis goals.  A limited offering of IPA will be sponsored by the CBC.  A training session by Qiagen will be announced in the upcoming weeks.
 
Need support?
Starting a new project or have one on the horizon?  Need a consultation, hardware access, or a piece of software installed on the cluster?  Fill out the account request/support form:
 
Want help from the comfort of your office? Ping us on our new Slack channel.  Anyone with a uconn.edu OR a uchc.edu address can join #bioinformatics_help using (uconn-cbc.slack.com)
 
Upcoming proposal? 
Request a letter from the CBC, Center for Genome Innovation (CGI), and/or the new Proteomics Core:
 
Recently published a manuscript that benefited from support or hardware at the CBC?  Please tell us!
 
Keep Connected/Updated!
Follow us on Twitter @UConn_Bioinfo
 
Subscribe to the mailing list (bioinformatics-L) here: https://listserv.uconn.edu/scripts/wa.exe?A0=BIOINFORMATICS-L

CBC Newsletter July 2017

July 2017 - Updates from the ISG Computational Biology Core (CBC)
 
Group Data Therapy Sessions - Biweekly on Fridays at 10:00am!
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.  We generally meet in BioPharm 203 (Storrs).  
 
We will be hosting our second UCH Data Therapy Session to provide an introduction to Unix, HPC and specifically the Xanadu cluster on Friday, July 28th at 10:00am.  
 
The following session (August 11th) will focus on Python for Bioinformatics
 
New Server - More Cores!  Welcome to Xanadu!
If you are seeking more resources - memory and cores - obtain a UCH account (CAM) here: http://bioinformatics.uconn.edu/contact-us/ (select UCH)
 
This will provide access to our new cluster Xanadu.  Xanadu utilizes Slurm rather than SGE for job management.  To learn how to access and interact with the Xanadu cluster, please go here:

Announcing Winter Workshops
CBC Workshops are offered across 2-3 full days (cost: $700).  They are open to advanced undergraduates, graduate students, postdocs, and faculty.  Each class enrolls a maximum of 10 students and provides hands-on training and background for genomics data analysis.  Use the following survey to tell us about the training you or your group members need.
 
ChIP-Seq: Experimental Design and Analysis
Dates: December 2017 (TBA)
Location: UCH Campus
 
Geneious!
The CBC is now hosting five commercial floating licenses for the Geneious software package.  To access these licenses - please follow the instructions posted here:
 
To learn more about Geneious, visit: http://www.geneious.com
 
Need Pathways?  Access GeneXPlain!
The CBC is hosting a site license for the GeneXPlain web-based platform that can be accessed here: http://genexplain.cam.uchc.edu/bioumlweb/
 
 
Login e-mail is your CAM username.
 
Note: You will need a UCH account (also known as a CAM account) to access Geneious and GeneXPlain. 
 
To obtain a UCH CAM account - go here: http://bioinformatics.uconn.edu/contact-us/ (select UCH)
 
Need support?
Starting a new project or have one on the horizon?  Need a consultation, hardware access, or a piece of software installed on the cluster?  Fill out the account request/support form:
 
Want help from the comfort of your office? Ping us on our new Slack channel.  Anyone with a uconn.edu OR a uchc.edu address can join #bioinformatics_help using (uconn-cbc.slack.com)
 
Upcoming proposal? 
Request a letter from the CBC, Center for Genome Innovation (CGI), and/or the new Proteomics Core:
 
Recently published a manuscript that benefited from support or hardware at the CBC?  Please tell us!
 
Keep Connected/Updated!
Follow us on Twitter @UConn_Bioinfo
 
Subscribe to the mailing list (bioinformatics-L) here: https://listserv.uconn.edu/scripts/wa.exe?A0=BIOINFORMATICS-L

CBC Newsletter May 2017

May 2017 - Updates from the ISG Computational Biology Core (CBC)
 
Group Data Therapy Sessions - Biweekly on Fridays at 10:00am!
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.  We generally meet in BioPharm 203 (Storrs).  
 
We will be hosting our first UCH Data Therapy Session to provide an introduction to HPC and specifically theXanadu cluster on Friday, June 2nd at 10:00am.  
 
The following session (June 16th) will focus on Metatranscriptomics and will held at back in BioPharm 203 in Storrs.
 
Announcing Bioinformatics Summer Workshops
CBC Workshops are offered across two full days (cost: $700).  They are open to advanced undergraduates, graduate students, postdocs, and faculty.  Each class enrolls a maximum of 10 students and provides hands-on training and background for genomics data analysis.  Use thefollowing survey to tell us about the training you or your group members need.
 
You can sign-up for two courses offered this summer:
 
RNA-Seq: Experimental Design and Analysis
Dates: July 20-21 2017, 9-5pm
Location: Beach Hall, Storrs Campus
 
ChIP-Seq: Experimental Design and Analysis
Dates: August 24-25 2017, 9-5pm
Location: Beach Hall, Storrs Campus
 
Geneious!
The CBC is now hosting five commercial floating licenses for the Geneious software package.  To access these licenses - please follow the instructions posted here:
 
To learn more about Geneious, visit: http://www.geneious.com
 
Need Pathways?  Access GeneXPlain!
The CBC is hosting a site license for the GeneXPlain web-based platform that can be accessed here: http://genexplain.cam.uchc.edu/bioumlweb/
 
 
Login e-mail is your CAM username.
 
Note: You will need a UCH account (also known as a CAM account) to access Geneious and GeneXPlain. 
 
To obtain a UCH CAM account - go here: http://bioinformatics.uconn.edu/contact-us/ (select UCH)
 
Need support?
Starting a new project or have one on the horizon?  Need a consultation, hardware access, or a piece of software installed on thecluster?  Fill out the account request/support form:
 
Want help from the comfort of your office? Ping us on our new Slack channel.  Anyone with a uconn.edu OR a uchc.edu address can join #bioinformatics_help using (uconn-cbc.slack.com)
 
Upcoming proposal? 
Request a letter from the CBC, Center for Genome Innovation (CGI), and/or the new Proteomics Core:
 
Recently published a manuscript that benefited from support or hardware at the CBC?  Please tell us!
 
Keep Connected/Updated!
Follow us on Twitter @UConn_Bioinfo
 
Subscribe to the mailing list (bioinformatics-L) here: https://listserv.uconn.edu/scripts/wa.exe?A0=BIOINFORMATICS-L
 

CBC Newsletter March 2017

March 2017 - Updates from the ISG Computational Biology Core (CBC)
 
Group Data Therapy Sessions - Biweekly on Fridays!
Bring your data woes to our next session Friday, March 24th.  Our next topic is RADSeq but these will change week to week depending on group input.  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.  We currently meet in BioPharm 203.
 
Announcing Bioinformatics Summer Workshops
CBC Workshops are offered across two full days (cost: $700).  They are open to advanced undergraduates, graduate students, postdocs, and faculty.  Each class enrolls a maximum of 10 students and provides hands-on training and background for genomics data analysis.  Use the following survey to tell us about the training you or your group members need.
 
You can sign-up for two courses offered this summer:
 
RNA-Seq: Experimental Design and Analysis
Dates: July 20-21 2017, 9-5pm
Location: Beach Hall, Storrs Campus
 
ChIP-Seq: Experimental Design and Analysis
Dates: August 24-25 2017, 9-5pm
Location: Beach Hall, Storrs Campus
 
Where are the applications?
We host hundreds of bioinformatics applications!  These applications are hosted on two different clusters (BBC and HPC1).  To find out how to access these applications, visit our software page: http://bioinformatics.uconn.edu/software/
 
FAST searches!
The CBC is now hosting Diamond indexes in addition to NCBI BLAST.  This similarity search package can align (long or short) sequences against the indexed database of your choice - at incredible speeds!
To learn more about Diamond: https://github.com/bbuchfink/diamond
Database indexes we are supporting: http://bioinformatics.uconn.edu/databases/
 
Need support?
Starting a new project or have one on the horizon?  Need a consultation, hardware access, or a piece of software installed on the cluster?  Fill out the account request/support form:
 
Want help from the comfort of your office? Ping us on our new Slack channel.  Anyone with a uconn.edu or a uchc.edu address can join #bioinformatics_help using (uconn-cbc.slack.com)
 
Upcoming proposal? 
Request a letter from the CBC, Center for Genome Innovation (CGI), and/or the new Proteomics Core:
 
Recently published a manuscript that benefited from support or hardware at the CBC?  Please tell us!
 
Keep Connected/Updated!
Follow us on Twitter @UConn_Bioinfo
 
Subscribe to the mailing list (bioinformatics-L) here: https://listserv.uconn.edu/scripts/wa.exe?A0=BIOINFORMATICS-L
 

CBC Newsletter January 2017

January 2017 - Updates from the ISG Computational Biology Core (CBC)

 
Expanding the CBC Team!
Two new members have recently joined the CBC team.  Dr. Vijender Singh joined in October 2016 as our new lead bioinformatics scientist.  He comes to us with several years of experience in genomics and bioinformatics from the Center of Gene Regulation and Expression at the University of Dundee.  Dr. Neranjan Perera joined us as a Postdoctoral Scholar in December 2016.  He recently obtained his PhD in Chemistry here at UConn and trained in the CBC for one year before joining.  Both of our new members are looking forward to working with you!
 
Starting this Friday, Feb 3rd: Group Data Therapy Sessions!
We will be leading hour long sessions every other Friday at 10am.  Bring your data woes to our first session this Friday, Feb. 3rd.    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.  We will reserve a room once we have an idea of how many of you need therapy.
 
Mark your Calendars!  COMPUTATIONAL BIOLOGY CORE OPEN HOUSE - FEBRUARY 24th 
9:30am - 4:30pm in the Genome and Cell Sciences Building at UCHC in Farmington.
This full day event will provide information on our new hardware capacities, software offerings/training, research talks, and details on the types of support provided by our team.  Lunch will be provided as well as shuttle transport from Storrs to UCHC.  A full schedule of events will be provided shortly!
 
Bioinformatics Summer Workshops
New CBC training workshops will be offered this summer.  These are offered as 2 or 3 full days (depending on the topic and level).  The courses will range in cost from $500-$700 and are open to undergraduates, graduate students, postdocs, and faculty.  We will be offering an RNA-Seq course this April and want to hear from you on other topics of interest!  Each class enrolls a maximum of 10 students and provides hands-on training and background for genomics data analysis.  Use the following survey to tell us about the training you or your group members need.
 
Need support?
Starting a new project or have one on the horizon?  Need a consultation, hardware access, or a piece of software installed on the cluster?  Fill out the account request/support form:
 
Want help from the comfort of your office? Ping us on our new Slack channel.  Anyone with a uconn.edu or a uchc.edu address can join #bioinformatics_help using (uconn-cbc.slack.com)
 
Upcoming proposal? 
Request a letter from the CBC, Center for Genome Innovation (CGI), and/or the new Proteomics Core:
 
Recently published a manuscript that benefited from support or hardware at the CBC?  Please tell us!
 
Keep Connected/Updated!
Follow us on Twitter @UConn_Bioinfo
 
Subscribe to the mailing list (bioinformatics-L) here: https://listserv.uconn.edu/scripts/wa.exe?A0=BIOINFORMATICS-L