For the past five years, Joan-Emma Shea, a professor at the University of California, Santa Barbara, has run thousands of amlyoid peptide simulations on the Ranger supercomputer at the Texas Advanced Computing Center (TACC) in an attempt to better understand Alzheimer's disease.

Shea is using the 579 teraflop supercomputer to look for data in support of the hypothesis that says toxcity in the brain is cause by small, transient molecules.

While the accumulation of amyloid plaques ‭ long knotty fibrils that result from misfolded proteins ‭ has long been associated with brain cell death, researchers have now begun to look at oligomers, the precursors of fibrils.

Her work is made possible with a grant from the National Institutes of Health and the National Science Foundation-funded Extreme Science and Engineering Discovery Environment (XSEDE) initiative, which aims to make computational resources widely available to the US research community.

Relatively speaking, a 579 teraflop supercomputer is not that impressive in a world where the fastest supercomputer currently clocks in at 16.32 petaflops. But this goes to show that the XSEDE program has the right stance in that researchers don't need the fanciest, fastest system in the world ‭ they just need easy access to a reliable HPC system with a respectable flops performance.

The Ranger supercomputer allows Shea to model or simulate what structures the amyloid peptides are adopting, at resolutions far exceeding what is possible experimentally.

"The number of atoms is huge•we need a lot of computational resources to simulate them. Nothing that we're doing here is something that we could do on our home clusters. The scale of it is intractable," says Shea. "With growing computational resources and capabilities, we'll be able to look at how these proteins interact with membranes...We're far away from simulating a whole cell, but we can start incorporating additional elements that may turn out to be important."

Ranger is a Linux-based system with eighty-two compute racks housing the quad-socket compute infrastructure that uses the Lustre file system across 72 I/O servers.

Soon, Shea will be able to take advantage of the TACC's "Stampede" supercomputer, which is slated to come online in early 2013 and will be 20 times more powerful than Ranger.

To submit a proposal to request an allocation, you can visit the XSEDE website.

The National Cancer Informatics Program, part of the National Cancer Institute, has a blog post describing its journey on the road to an open-development software ecosystem.

Juli Klemm, associate director of Integrative Cancer Research Products and Programs at the Center for Biomedical Informatics and Information Technology at NCI, writes that for more than two years, she and her colleagues have been discussing and thinking about how to create such an ecosystem around the digital resources developed through the caBIG program.

They are not starting from scratch — the caBIG program is already open-source, with the "caBIG Open Source License" that allows users to download and alter code to suit their needs.

"We recognize that meeting the challenge of creating robust and useful tools to support the rapidly evolving needs of the cancer research community requires an open and collaborative approach to software development," Klemm writes.

NCI has looked to a number of similar efforts to help them build a roadmap for how to create this ecosystem. Their role models have included the open-development efforts of the Veteran's Administration and NASA as well as the open-source efforts of Apache, Mozilla, and Google.

In June of 2011, the NCIP issued an RFI in an attempt to collect input from the community on what their open-development ecosystem should look like.

While they only received 20 responses, Klemm writes that some of the respondents joined them at their Rockville offices and formed a sort of open-source think tank.

Click here to read the results of the meeting and what guidelines Klemm and her colleagues are moving forward with.

A new tool developed by a team at the Texas Advanced Computing Center promises to make scientific computing via web interfaces easier and more powerful.

Called the AGAVE API — A Grid and Virtualization Environment — this programming tool allows developers and users to launch a computational experiment using supercomputing resources in a relatively seamless fashion.

"When services have been built to that level, research starts moving really fast," says Rion Dooley, a research associate at TACC and one of the creators of the API. "You can start leveraging manpower and focus exclusively on the science rather than the computation and technology needed to accomplish that science."

For software developers, the AGAVE API provides a way for tools to be added to Web interfaces as well as data management offload and experiment execution with some line coding using a supercomputer.

For users, the AGAVE API essentially provides a science-as-a-service.

This API is currently being used within the iPlant project, which allows users to take advantage of compute resources at the Pittsburgh Supercomputing Center, San Diego Supercomputing Center, and TACC through the XSEDE project.

The developers of the BioExtract Server — a distributed database that consolidates data from heterogeneous bimolecular databases — are also using the AGAVE API to help scale out their resource to meet the demands of bioinformatics researchers.

A group of software developers from the University of Alabama at Birmingham have designed an image analysis app that functions just like Angry Birds or Instagram.

Their new app — called ImageJS — is described in a recent paper published in the Journal of Pathology Informatics entitled "ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser."

ImageJS allows pathologists to analyze digital pathology slides in a Web browser app where it can be analyzed for evidence of tumor cell growth.

"ImageJS" gets its name from "ImageJ," an image-analysis application developed by the National Institutes of Health that was written using the JAVA language — and which allegedly took hours to program and integrate into a hospital's patient data system.

Here's a demonstration of ImageJS:

According to the team, led by Jonas Almeida, director of the Division of Informatics in the UAB School of Medicine's Department of Pathology, the pathology modules are only the first in a series that will eventually include genomics analysis capabilities. The idea is that enabling such quick-and-easy comparisons will increase diagnostic accuracy and improve treatment plans.

Almeida and his team hope that pathologists will take this app and run with it, partnering with bioinformaticians to create other modules using the ImageJS open-source code.

ImageJS is currently available from the Google Chrome App store, Google Code and Github.

Intel has teamed up with NextBio in a collaboration focused on perfecting the Hadoop stack for analyzing large-scale genomic datasets.

Hadoop is a Java-based programming framework that supports the processing of large datasets in a distributed computing environment. It was originally developed by Google and then later picked up and developed for enterprise scenarios by Yahoo.

Engineering teams from NextBio and Intel say they will offer up their solutions and innovations to the open-source community once completed.

In the quotes below, the phrase "big data" is apparently now being referred to as "Big Data" — with a capital "B" and "D." This IT marketing neologism is meant to ensure that proper respect is given to this data — which is of a very big nature.

"Intel is firmly committed to the wide adoption and use of Big Data technologies such as [the Hadoop Distributed File System], Hadoop, and HBase across all industries that need to analyze large amounts of data," says Girish Juneja, CTO and General Manager of Big Data Software and Services at Intel. "Complex data requiring compute-intensive analysis needs not only Big Data open source, but a combination of hardware and software management optimizations to help deliver needed scale with a high return on investment. Intel is working closely with NextBio to deliver this showcase reference to the Big Data community and life science industry."

Don't have your Red Hat engineer certification yet but need to setup a Linux server? No problem, says an article over at Infoworld, you can just spin up your own using a release called "TurnKey Linux" on Amazon's cloud.

They walk you through the process of establishing this flavor of Linux on the cloud step-by-step here.

While TurnKey Linux can run on any ordinary server, Infoworld says it can be "mindlessly" setup on Amazon's cloud in under one hour. Chances are that even a Red Hat expert would be hard pressed to make everything work flawlessly in under 60 minutes, but TurnKey is an interesting offering nonetheless.

It will soon be released with a version built upon Debian Squeeze, a reportedly very stable version of the Linux kernel. And this version actually comes in an assortment of prepackaged, ready-to-use servers including Linux Apache, MySQL, PHP/Python/Perl, just to name a few.

Get your stopwatches ready and good luck.