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Author Archives: Dan Gezelter
Open Science talk at the 2014 NIAID bioinformatics festival
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.
Posted in Open Access, Open Data, open science, Policy, Science
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TeraPy
TeraPy is a graphical user interface for terahertz time-domain spectroscopy and other sequential measurements processes. Find TeraPy at: http://pythonhosted.org/terapy/
Posted in Condensed Matter, Spectroscopy
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OpenMD
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, … Continue reading
Posted in Molecular Dynamics
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SPINA: Structure parameter inference approach
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. … Continue reading
Posted in Medical Sciences
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New PLOS Open data policy
PLOS 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 … Continue reading
Posted in Open Access, Open Data, open science, Software
Tagged open science, open source software
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CloudSim
A Java Framework For Modeling And Simulation Of Cloud Computing Infrastructures And Services. Find CloudSim at: http://www.cloudbus.org/cloudsim/
Posted in Computer Science
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GENtle2
An updated, open source (MPL 2.0), web-based version of GENtle. Find GENtle2 at: http://gentledna.org
Posted in Bioinformatics
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EPANET
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 … Continue reading
Posted in Engineering
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On the Science “Sting”
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 … Continue reading
Posted in Open Access, Science
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A simple-r Linux command line R environment for statistical analysis
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 … Continue reading
Posted in Statistics
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