HPDA Orchestrator - Platform LSF

With the success of applying Platform Computing stack to genomics and growing number of scientific disciplines and other fields such as big data analytics, I was frequently asked about the scope and efforts it will take to migrate to or adopt Platform LSF. Below I will compile some documentation and best practice as a reference point:

PBS/Torque to LSF Migration Manual
This is a useful document showing how Durham University migrated from PBS/Torque to LSF. The manual was originally from here

LSF Migration Guide
This is a quick reference to assist system administrator or application support staff in converting MOAB scripts to LSF scripts

Download LSF DRMAA

The latest Platform LSF version has support for DRMAA, which can be downloaded in the link above.

 
If you have produced similar documentation and would like to share with the scientific community, please send it to me at drfranknlee@gmail.com

Sequence the City

Starting today at the IBM Almaden Research Center, scores of scientists and researchers are gathering for a two-day symposium called "Sequence the City: Metagenomics in the Era of Big Data."

The goal of the symposium? To explore how pervasive DNA sequencing across a city (or factory, farm, air travel system, etc.) could support a robust framework for safeguarding human and environmental health. The overarching aim is to articulate the promise and the challenge of genomics in the era of big data.

Metagenomics is the study of mixtures of genetic material corresponding to communities of bacteria, fungi, viruses, and other living things, often co-existing in a microenvironment like on a countertop or in the human gastrointestinal tract. Results from metagenomics research are leading to a new appreciation for the critical role that microbes play in the health of people and the environment. Continued advances in DNA sequencing technology and laboratory sample preparation make it possible to track microbes as they live amongst us, from the typical species and strains, to the malevolent needles in the haystack.

Genomic analysis of food, water, waste, soil, crops, insects, and swabbed surfaces from natural and built environments could provide advanced warning of threats to public health. Biosurveillance and diagnostics applications using DNA sequencing technology will require new algorithms and computational methods. Built upon new I/T services, software applications that digitally identify microbes may replace labor-intensive and time-consuming biochemical assays, effectively moving detection from the wet bench to the computer.

The symposium will focus on a broad spectrum of science and computational topics including the human microbiome, bacterial and viral evolution, agriculture, food safety, and the microbial ecology of buildings (e.g., factories) and even entire cities. The researchers will review some of the computational methods and analyses that are applied to genomic data today, and explore how new genomic data and services in the cloud could enable entirely new applications in the future.

Here is a report on the event from CNET.