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MiniLIMS: The Affordable Solution for Next-Gen Sequencing Data Management
Sponsored by BioTeam

Recorded on April 17, 2012 | DVD or Electronic Version for Purchase: $295   

With the incredible explosion in the throughput of next-gen sequencing (NGS) instrumentation, an increasingly critical component of any NGS workflow is the choice of LIMS (Lab Inf Mgt System). The appropriate choice of LIMS is essential to manage and schedule experiments, particularly between multiple groups/users, monitor progress, and collate and distribute the data.

The choice of LIMS for NGS applications has grown in recent years, but while there are many excellent choices on the market, they are typically compromised by either a lack of flexibility and/or a steep price tag – in some cases costing more than the actual sequencer it manages.

BioTeam – a successful group of IT consultants for academic and commercial life sciences organizations – has created an attractive alternative: MiniLIMS. The MiniLIMS system is a super flexible, lightweight data management system inspired by NoSQL and semantic web architectures – all of which are totally invisible to the user. MiniLIMS offers ease of use, abundant flexibility, …. All at a price beginning at a mere $5,000.

In this web symposium, you’ll hear from three academic organizations who are all applying MiniLIMS to the challenges of the rapidly changing NGS world. Attendees will learn how easy it is to import a variety of data (not just NGS) and how flexible it is to display and produce summaries. Additionally attendees will see how easy it is to extend the system for local lab needs and how to easily configure many of MiniLIMS’ elements.

A pair of case studies will be presented -- one for the NGS core sequencing facility at Harvard University and one for small-molecule mass spectrometry also at Harvard. Topics to be covered include:

  • Importing and exporting data
  • User permissions - restricting access to private data.
  • Navigation and configuration of the data display
  • Setting up email and sms alerts when certain fields change
  • Adding new data types and values to existing pages
  • Adding completely new types of data and seamlessly integrate them into the GUI

Speakers:
Aaron Kitzmiller (Senior Scientific Consultant, BioTeam)
Michelle Clamp (Dir Informatics, Harvard University)
Greg Harhay (USDA MARC)

Speaker Bios:

Aaron Kitzmiller 

Aaron’s 15 years in the development of scientific software began during his Neurosciences PhD at the University of North Carolina, but quickly turned toward genomics and bioinformatics.  While working first in the pharmaceutical industry and later in next gen sequencing companies, he’s developed solutions within many of the major threads of the last decade of bioinformatics (EST mining; genome and Affy array annotation; analysis and execution frameworks; text mining; chemical and biological data integration; short read analysis) in a variety of technological contexts (Java GUIs; Oracle and MySQL database systems; SMP machines; 3 tiered Web architectures; compute clusters; command line tools; Web 2.0; cloud computing).  His biggest pleasure is in the development of simple software tools that make analysis and data accessible to the growing number of scientists that can no longer get by on Excel alone.

Michelle Clamp
After studying physics at Oxford University and obtaining a PhD from Manchester University, Michele discovered the exciting field of computational biology through modeling protein structure. She spent some 15 years in high-throughput bioinformatics analysis at Oxford, developing popular visualization tools. She is also a co-founder of the EnsEMBL genome annotation database. She spent six years at the Broad Institute studying human gene annotation and comparative genomics with Eric Lander. Two years ago, she joined BioTeam, where she was instrumental in the creation of MiniLIMS. She was recently appointed as Director of Informatics and Scientific Applications at Harvard University.

Greg Harhay
Greg Harhay is a Computational Biologist in the Animal Health Research Unit at the United States Meat Animal Research Center (USMARC) in Clay Center, NE.  Greg received his doctorate in chemistry at the University of Oregon and was a post-doctoral fellow at Brookhaven National Lab before joining USMARC, where he has focused on applying computational “Omics” approaches to address problems in livestock production and health, and microbial genomics.  He leads efforts at USMARC to develop and maintain an on-site computational infrastructure for managing and analyzing next-gen sequencing data.  He is currently applying host and pathogen genomic investigations to address problems in ruminant respiratory diseases.

DVD or Electronic Version for Purchase: $295 

 


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