We'd like to foster more communication among MacResearch participants, so we're considering how a mailing list or lists could help the MR community. There's a poll that's active right now, wondering whether a single mailing list of anyone interested, subject specific lists, both, or no lists is the preferred way to host a mail solution.
We're very interested in doing what the community wants, so please take some time and respond to the poll. I'll also be reading responses to this post, to figure out what the right solution for MR mail is. Please give us feedback so we can make MR a community that works the way you want to see it work.
Continuing the trend of recent news for MacIntel compilers, Intel has just released the Fortran Compiler 9.1 for Mac OS. The professional edition is being sold at a discount until the end of the year.
Those of you using the Intel C++ beta compiler may have already heard about this. For those of you not participating in that program, Intel has announced a new beta program for their Intel Threading Building Blocks. The idea behind this is that multithreading common tasks can be abstracted away from low level threading details; the developer will specify threading by task rather than coding specific threading information (the compiler and libraries will take care of the details). This reminds me somewhat of the OpenMP programming model for shared memory systems.
The Intel Threading Building Blocks are designed to thread for performance (that is, computationally intensive tasks), can co-exist with other threading packages and, according to the manual, utilizes a generic programming model "where interfaces are specified by requirements on types". In addition to the manual, the install includes a tutorial PDF to help get you started. The Intel Threading Building Blocks are cross platform, support 32-bit/64-bit applications and work with Intel, Microsoft and GNU compilers. The beta is open to everyone.
Adium is a collaboration tool that could be incredibly useful to some. Its instant messaging with a twist: the capability of entering equations using LaTeX! You can find out more about this feature and see a screenshot here or just try Adium yourself by visiting AdiumX.com. Enjoy!
Mek & Tosj would like to announce a completely rewritten version of one their most popular programs, EnzymeX. EnzymeX has become a favorite tool of many molecular biologists using a mac. It is a program developed to help them determine which restriction enzymes they should use to cut their DNA of interest. In addition, it gives all the specific properties of these enzymes to make sure that every digestion is a success.
One of the most requested features people wanted to see in EnzymeX was the ability to load their DNA of interest and analyze where exactly the different enzymes would cut. Sure there are other programs that can do this, but why do they have to look like coming straight from the 1980's or from another platform? Now the long wait is over and we have finally created a DNA sequence editor that brings all those features and the look and feel you can expect to come with a true MacOSX program.
Here are a few of the main new features in EnzymeX 3:
- Support of many DNA sequence formats through the BioCocoa core
- Direct download of sequences from NCBI's Entrez DNA database
- Finding of Open Reading Frames and translation from DNA to Protein
- Enzyme Restriction maps
- Smart Quick Search, with Motifs searches
- Mini enzyme inspector showing all the enzyme info you ever need
- EnzymeX plugin architecture for custom extensions
- And much much more...
We've spent the past three days here in Cupertino locked up in the Apple Developer Connection Labs talking with alot of Apple folks about issues that affect the MacResearch Community. We did this jointly with the MacEnterprise folks and it turned out to be an extremely productive time. While there are definitely issues that need to be dealt with for the transition -- almost all of them appear to be issues with third party applications -- the transition to the intel processors is happening remarkably smoothly.
Just a quick note. Many people on our survey have noted that they need Fortran compilers (a free compiler in addition to a high performance compiler from Intel). A build of gfortran is now available. Please see the following website (and great all around resource!). There currently doesn't appear to be a g77 build which I'm sure a lot of people would like to have as well (I would). But at least there are a couple of options for fortran code now.
I'd be curious to hear comments on the Clearspeed math processor and its ilk. As a starter link, this discussion at ArsTechnica mentionds that AMD is looking to pair this with their quad Opteron machine.
Interestingly for Mac users, one of the articles linked therein has this:
"Interestingly, it's not just AMD who's taken an interest in Clearspeed. Last week, Intel co-published a paper on using Clearspeed's twin-chip Advance board to boost Intel Math Kernel Library operations significantly."
Those who like speculating on future hardware (or playing around with hardware) might like to wonder what they could do with a ClearSpeed math processor on an Intel Mac...?
For my money, the key to making this sort of thing work, would be to leverage the math processor via libraries, so that most developers don't have to directly deal with the math processor.
I just stumbled across this electronic LabBook from the University of Utah written in Python:
It provides a laboratory with a central storage place for electronic files from experiments, it is searchable, has a todo-list with calendar function, a user administration and is accessed through a web browser.
It is very straight forward and considering that this is version 1.0 promising at the same time.
Aborygen, the company behind the commercial bioinformatics application biOpen®, have quietly expanded their selection of free Dashboard widgets for bioinformatics. There are some really handy reference widgets available, such as the Genetic Code and Amino Acid Table widgets. Several of the widgets, like the SpectroConverter and DNA/Protein Converter widgets, provide helpful utility functions. For a full list of available utilities visit the Aborygen widget download page.