Open Science talk at the 2014 NIAID bioinformatics festival

Posted on April 8, 2014 by Dan Gezelter

Dan is giving a talk today at the 2014 NIAID bioinformatics festival.  The meeting is being live streamed from the NIH campus. If you’d like a preview, the slides are now available on slideshare.

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Posted in Open Access, Open Data, open science, Policy, Science | Leave a comment

TeraPy

Posted on April 6, 2014 by Dan Gezelter

TeraPy is a graphical user interface for terahertz time-domain spectroscopy and other sequential measurements processes.
Find TeraPy at: http://pythonhosted.org/terapy/

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Posted in Condensed Matter, Spectroscopy | Leave a comment

OpenMD

Posted on April 4, 2014 by Dan Gezelter

OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. sticky atoms, point dipoles, and coarse-grained assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat interfaces, and nanoparticles) have all been simulated using force fields included with the code. OpenMD works on parallel computers using the Message Passing Interface (MPI), and comes with a number of analysis and utility programs that are easy to use and modify. An OpenMD simulation is specified using a very simple meta-data language that is easy to learn.
Find OpenMD at: http://openmd.org

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SPINA: Structure parameter inference approach

Posted on April 3, 2014 by Dan Gezelter

SPINA (structure parameter inference approach) is a method that allows for calculating constant structure parameters of endocrine feedback control systems in vivo from hormone levels obtained from serum or plasma. A first successful implementation applies to evaluation of thyroid function. It allows for calculating the thyroid’s maximum secretory capacity (GT or SPINA-GT) and the sum activity of peripheral 5′-deiodinases (GD or SPINA-GD) from levels of TSH, (F)T4 and (F)T3 that have been determined once only (SPINA Thyr). This method is increasingly used in experimental research. SPINA Thyr has been evaluated in clinical trials covering more than 9000 subjects with various disorders of thyroid homeostais. Additional applications targeting other endocrine feedback loops are currently being developed or prepared, respectively. SPINA Thyr is a free application that calculates GT and GD. It is offered on the base of a BSD licence. Binaries are available for Mac OS, Mac OS X, Palm OS, Garnet OS and Windows. For other operating systems, including Linux, Solaris and BSD, SPINA Thyr is available as sourcecode. Building from source requires THINK Pascal (for Mac OS Classic), winsoft PocketStudio (for Palm OS / Garnet OS) or Lazarus/Free Pascal (for Mac OS X, Windows, Linux, BSD and Solaris). A special version of the calculation engine is available for modern S implementation, e.g. R.
Find SPINA: Structure parameter inference approach at: http://spina.sf.net

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New PLOS Open data policy

Posted on February 25, 2014 by Dan Gezelter

PLOS one logoPLOS has announced some changes to their publishing policies, and these changes are great news.  The new PLOS policies will go a significant way towards encouraging open data and open source.  Although the announcement itself is somewhat vague on the subject of source code, the actual PLOS One Sharing Policy is excellent:

…if new software or a new algorithm is central to a PLOS paper, the authors must confirm that the software conforms to the Open Source Definition, have deposited the following three items in an open software archive, and included in the submission as Supporting Information:

  • The associated source code of the software described by the paper. This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL, or MIT (see http://www.opensource.org/licenses/alphabetical for a full list). Dependency on commercial software such as Mathematica and MATLAB does not preclude a paper from consideration, although complete open source solutions are preferred.
  • Documentation for running and installing the software. For end-user applications, instructions for installing and using the software are prerequisite; for software libraries, instructions for using the application program interface are prerequisite.
  • A test dataset with associated control parameter settings. Where feasible, results from standard test sets should be included. Where possible, test data should not have any dependencies — for example, a database dump.

However, the one loophole is that they allow for code that runs on closed source platforms in “common use by the readership”  (e.g. MATLAB), although it must run without dependencies on proprietary or otherwise unobtainable ancillary software.  That “common use” loophole could potentially be a mile wide in some fields.  Is Gaussian a common use platform in computational chemistry and therefore exempt from this new policy?   If so, the policy is a bit toothless.  I’d like to see the limits and bounds of the “common use” loophole more clearly stated.

The announcement makes PLOS ONE a much more attractive place to send our next paper.

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CloudSim

Posted on October 31, 2013 by Dan Gezelter

A Java Framework For Modeling And Simulation Of Cloud Computing Infrastructures And Services.
Find CloudSim at: http://www.cloudbus.org/cloudsim/

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GENtle2

Posted on October 21, 2013 by Dan Gezelter

An updated, open source (MPL 2.0), web-based version of GENtle.
Find GENtle2 at: http://gentledna.org

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EPANET

Posted on October 7, 2013 by Dan Gezelter

EPANET is software that models water distribution piping systems. EPANET is public domain software that may be freely copied and distributed. It is a Windows 95/98/NT/XP program. EPANET performs extended period simulation of the water movement and quality behavior within pressurized pipe networks. Pipe networks consist of pipes, nodes (junctions), pumps, valves, and storage tanks or reservoirs. EPANET tracks: – the flow of water in each pipe, – the pressure at each node, – the height of the water in each tank, and – the type of chemical concentration throughout the network during a simulation period, – water age, – source, and – tracing.
Find EPANET at: http://www.epa.gov/nrmrl/wswrd/dw/epanet.html

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On the Science “Sting”

Posted on October 3, 2013 by Dan Gezelter

Science magazine (a closed-access publisher) does a “sting” on crappy OA journals (and boy are there lots of these), and Michael Eisen points out how this sting is more about how crappy peer review is at catching bad science (even at Science).  Here’s the best quote from Eisen’s response:

“To suggest – as Science (though not Bohannon) are trying to do – that the problem with scientific publishing is that open access enables internet scamming is like saying that the problem with the international finance system is that it enables Nigerian wire transfer scams.

There are deep problems with science publishing. But the way to fix this is not to curtain open access publishing. It is to fix peer review.”

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A simple-r Linux command line R environment for statistical analysis

Posted on October 2, 2013 by Dan Gezelter

The program is a simple wrapper to use R functions on a single text file from the command line; useful for quick data plotting or statistical analysis. The program generates and runs R script that: (a) loads up data from the file as a single data frame assuming default parameters (b) runs R functions, described by preset options or passed directly to the script. It should be helpful for anybody who is using a lot of Linux command line for statistical analysis.
Find A simple-r Linux command line R environment for statistical analysis at: http://code.google.com/p/simple-r/

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Posted in Statistics | Leave a comment