Practical Computing for Biologists

This book teaches computer skills to biologists by focusing on topics and techniques that are applicable to a range of bio-infomatics endeavors. These topics include:

Searching with regular expressions
The Unix command line
Python programming and debugging
Creating and editing graphics
Databases
Performing analyses on remote servers
Working with electronics

The main narrative focuses on Mac OS X.

The book is designed to be used as a self-guided resource for researchers, a companion book in a course, or as a primary textbook.

Find it @ http://www.amazon.com/Practical-Computing-Biologists-Steven-Haddock/dp/product-description/0878933913/ref=dp_proddesc_0?ie=UTF8&n=283155&s=books

Wednesday, March 23, 2011

Gladinet Cloud Desktop

Gladinet Cloud Desktop is a Windows client software that enables seamless access, aggregation, and backup to cloud storage sites. The following are supported:

  1. Amazon S3
  2. AT&T Synaptic Storage
  3. Caringo CAStor
  4. EMC Atmos Online
  5. Google Storage
  6. Nirvanix
  7. Mezeo
  8. Windows/Azure
  9. Box.net
  10. OpenStack
  11. Peer1 CloudOne
  12. Rackspace CloudFiles
  13. FTP
  14. WebDav

Find it @ http://www.gladinet.com/p/moreaboutdesktop.htm

There is a free starter edition for non-commercial use.

The licensing information may be found @ http://www.gladinet.com/gladwiki/moin.cgi/Gladinet_CloudDesktop_License

XMind

This is mind mapping tool similar to the MindManager from MindJet and MS Visio's BarinStorming feature.

It is very easy to use and intuitive.

Watching diagrams is usually more effective that reading the prose.

The disadvantage is that the free version of the application has limited export features, but there is a possibility to put the body into a Word document

You can download XMind free version from http://www.xmind.net/.

NHTSA-NASA Study of Unintended Acceleration in Toyota Vehicles

NHTSA-NASA Study of Unintended Acceleration in Toyota Vehicles @ http://www.nhtsa.gov/UA

The report may be found @ http://www.nhtsa.gov/staticfiles/nvs/pdf/NHTSA-UA_report.pdf

NASA team applied static source-code analysis, formal logic model checking, and algorithm analysis through simulation.

The report states "The team's experience is that there is no single analysis technique today that can reliably intercept all vulnerabilities, but that it is strongly recommended to deploy a range of different leading tools."

For code analysis, the team used Coverity, CodeSonar, and Bell Labs' Uno to identify common coding defects and suspicious coding patterns. The team also used CodeSonar to compare Toyota's code against a Jet Propulsion Lab coding standards (1,2,3).

For model checking, the team used open-source Spin and Swarm. To use a formal model checker, one first has to write formal models. The team built models only for those software modules it believed could be culprits; the formal analysis depended on human judgment.

The algorithm analysis began with building models in Matlab. This process started with reading Toyota documentation and talking with Toyota engineers, and then progressed to analyzing the source code and finally testing the models against actual Camrys. Once the NASA team was satisfied with the models, they explored failure scenarios in Simulink and checked delays with AbsInt aiT.

Some conclusions suggest themselves. First, there are no silver bullets: effective debug means using everything you've got.

Second, even when it's grounded in exhaustive and formal techniques, an evaluation is circumscribed by the evaluators' beliefs about the possible behavior of the system.

Third, there is no certainty. Despite Toyota's great care in developing their code, NASA's analysis found significant errors, including serious underestimates of delays in the multiprocessing system.

But the investigation could not link those errors to any proposed mechanism for unintended acceleration. NASA Executive Summary stated "Because proof that the ETCS-i caused the reported UAs [unintended accelerations] was not found does not mean it could not occur."