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Release of libsoc (0.6) with ability to reference PharmML files

posted Jan 13, 2018, 5:33 AM by Maciek J Swat

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)

posted Aug 22, 2017, 7:01 AM by Maciek J Swat   [ updated Aug 22, 2017, 7:02 AM ]

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

posted Feb 9, 2017, 1:25 AM by Maciek J Swat   [ updated Feb 9, 2017, 1:25 AM ]

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:
  • Discrete univariates  36
  • Continuous univariates  99
  • Mixture univariate  1
  • Discrete multivariates   1
  • Continuous multivariates 13
  • Empirical/Samples  3
  • TOTAL 153

For more details see www.probonto.org

PharmML/SO talk at Combine 2016

posted Sep 23, 2016, 1:48 AM by Maciek J Swat

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!

posted Jul 22, 2016, 5:54 AM by Maciek J Swat

New in this version:
  1. Mixture models 
    • mixtures of distributions
    • mixtures of structural models (wsmm, bsmm)
  2. New DE notation - encodable are ODEs, DDEs & PDEs with boundary and initial conditions
  3. Autocorrelation models of residual errors
  4. BoxCox2 & user-defined transformations
  5. User-defined distributions
  6. Updated covariates, occasions and design spaces handling in TD
  7. Exclusion and inclusion criteria for covariates
  8. Categorical covariates building (clustering)
  9. Observation model extensions - multiple models and models in conditionals permitted
  10. Tool-specific settings support
  11. Other minor extensions and changes
See for details the attached spec document.
New ProbOnto 2.0 schema for PharmML has been released separately

ProbOnto 2.0 is out

posted Jul 20, 2016, 11:57 PM by Maciek J Swat

...with new 
  • distributions (such as LogNormal7, parameterisation used in PopED, Trapezoidal1, HalfNormal2 and WienerDiffusionModel1)
  • relationships (mostly re-parameterisations for LN7) and 
  • survival and hazard functions - see Exponential1 and Weibull1 for their plots
  • changes to namespaces and ID convention
See the website probonto.org for more details.

BMSS/SOT PharmML webinar - Friday, 22nd July

posted Jul 14, 2016, 3:07 AM by Maciek J Swat   [ updated Jul 14, 2016, 3:08 AM ]

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!

posted Mar 24, 2016, 4:56 AM by Maciek J Swat   [ updated Mar 24, 2016, 4:57 AM ]

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:
  1. Over 80 uni- and multivariate distributions and alternative parameterisations.
  2. Probability density or mass functions and where available cumulative distribution, hazard and survival functions.
  3. Supports encoding of univariate mixture distributions.
  4. Over 130 relationships and re-parameterisation formulas.
  5. Related quantities such as mean, median, mode, variance.
  6. Parameter and support/range definitions and distribution type.
  7. Latex and R code for mathematical functions.
ProbOnto has been in use in PharmML since version 0.7.1. 

See for more details probonto.org

PharmML v0.8

posted Jan 13, 2016, 9:13 AM by Maciek J Swat   [ updated Jan 13, 2016, 9:13 AM ]

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

posted Sep 14, 2015, 2:48 AM by Maciek J Swat

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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