News
Release of libsoc (0.6) with ability to reference PharmML files
We are happy to announce that a new version of libsoc (0.6), the R package for reading and writing SO files, has been released to CRAN, provided by Rikard Nordgren from Uppsala University. The most important addition is functions to use a referenced PharmML to get information on types of parameters, i.e. if a parameter is structural, connected to residual variability or parameter variability, if a parameter is a correlation and which random variable (ETA) a variability parameter is connected to. Read examples in the new vignette (see link below). The latest version of nmoutput2so (4.7.12) has an option (-generate_pharmml) to generate a minimal PharmML with information on the parameter model to be used by libsoc. The new vignette for an introduction to reading SO-files: https://lnkd.in/e4Xd3Qm Detailed list of changes can be found here: https://lnkd.in/ecfsRhZ |
First release of pharmmlutils (pharmmltool)
We are happy do announce the first release of pharmmlutils by Rikard Nordgren (Uppsala University), that currently contain pharmmltool. pharmmltool is a utility to validate PharmML 0.8.1 and 0.9, convert from PharmML 0.6 to 0.8.1 or 0.9 and 0.8.1 to 0.9. It can also strip spaces, add indentation and print the version of a PharmML file. See the README for more details. Packages for Linux, Mac and Windows can be found at https://github.com/rikardn/libpharmmlcpp/releases |
ProbOnto 2.5 release
New in this release: - 44 additional uni- and multivariate distributions - Relationships/re-parameterisations, HFs and SFs - Model definitions added for the majority of distributions - Few bugs/typos fixed - see spec for details Current count:
For more details see www.probonto.org |
PharmML/SO talk at Combine 2016
PharmML & SO has been presented by Maciej J Swat at the COMBINE 2016 meeting in Newcastle upon Tyne (UK). Slides can be downloaded from DropBox: tinyurl.com/hl7atym |
PharmML 0.9 is out!
New in this version:
New ProbOnto 2.0 schema for PharmML has been released separately |
ProbOnto 2.0 is out
...with new
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BMSS/SOT PharmML webinar - Friday, 22nd July
Don’t miss the PharmML webinar (22 July 11:00 AM EDT / 4:00 PM CET) organised by Biological Modeling Specialty Section (BMSS) of the Society of Toxicology (SOT). PharmML, SO and ProbOnto will be presented with use cases. URL: https://www.toxicology.org/groups/ss/BMSS/index.asp#Events |
ProbOnto paper accepted for publication!
An application note on ProbOnto 1.0 has been accepted for publication in Bioinformatics! ProbOnto stands for 'Ontology and Knowledge Base of Probability Distributions' and has following features:
ProbOnto has been in use in PharmML since version 0.7.1. See for more details probonto.org |
PharmML v0.8
New version of PharmML v0.8 is ready to download - with support for (optimal) trial design, Bayesian inference etc. It is a development version meaning no full spec is available. Only a detailed changes document has ben released. Your feedback is very welcome! |
PharmML - Europe's 'top' markup language
On Thursday, September 10th, PharmML logo was spotted on Mont Blanc, 4810 m, see 'Home' page. We had temperatures about -12C but otherwise great weather which made it possible. Back to the office now and working on the next release. |
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