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Informatics at CIDR

 

CIDR has a multi-disciplinary informatics team led by Lee Watkins Jr., Director of BioInformatics & IT, Sean Griffith, Informatics Software Project Manager, and Elvin Hsu, IT Systems & Support Manager. In addition to bioinformatics, database, systems, and user support professionals, our software development group designs custom solutions for internal clients. Using a team-based, flexible development methodology, the software development team -- fluent in Java, Python, hibernate, JDBC, Django, Perl, JavaScript, SQL and shell scripting -- works collaboratively with colleagues to build and maintain a variety of essential tools to support CIDR's genotyping and next-generation sequencing services:

 


CIDR Software

Because of CIDR's high throughput, quality control standards, and customized services, off-the-shelf software products do not always meet our needs. When it is not possible to integrate a third-party software into our workflows, CIDR's in-house software development team creates solutions for our lab, data analysts, project managers and statistical geneticists. Read about some of them here.

 

Informatics Infrastructure

To meet the enormous computational and data management challenges created by genotyping and sequencing over 100,000 samples per year, we have continuously expanded and improved our informatics infrastructure, described in detail here. We also have access to the new Maryland Advanced Research Computing Center (MARCC) on the Hopkins Bayview campus. This HPC facility opened in May 2015 with over 19,000 cores (including large-memory and GPU nodes), 20 petabytes of storage and 100 gigabits/second network connectivety, with a CLIA-certifiable platform to be available to us in mid-2016.

 

Scientific Posters
CIDR informatics staff have presented more than 20 posters at scientific conferences. You can find most of them here.

 

Technical Reports

CIDR informatics staff, working closely with laboratory and scientific colleagues, regularly conduct technology evaluation projects that, if successful, may result in new production processes or systems. When appropriate and time permits, a project technical report is produced to share what we've learned:

Implementing a Third-Party Inventory System at CIDR

 

Contact Us!

Please feel free to contact us if you are a CIDR project investigator with any questions or concerns, are interested in our informatics tools or services or in pursuing potential collaborations. We can most easily be reached at cidr_informatics@lists.johnshopkins.edu

 

 

 

 

 

 

 

 

 


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photo of IT staff

 

CIDR informatics Staff (left to right) Elvin Hsu, Filipp Kistenev, Kurt Hetrick, Dean Snyder, Kevin Duerr, Sean Griffith, Brad Tibbils, Lee Watkins Jr., Ben Myers,Greg Lowe and Sunny Sun. Not pictured: Earl Elias, Laura Miedzianowski, Keith Roberts, Alice Sanchez