Physiome Project

  • The Physiome Project aims to provide a quantitative modeling framework for understanding whole body function
  • The Physiome Model Repository contains over 700 models of physiological processes encoded in reproducible form
  • Physiome is a journal that publishes the curated, annotated and documented version of a model or models associated with a primary publication in an existing physiology, bioengineering, biophysical or biomathematical journal

The mammalian body is a highly integrated system in which every organ communicates with every other organ via the vasculature, the autonomic nervous system and, to some extent, via the musculo-skeletal system. Every gene potentially, therefore, has an influence on every organ and as a consequence every physiological phenotype may be influenced by the entire genome.

One of the major challenges facing physiology, therefore, is that of linking organism–wide physiological function, or dysfunction in the case of disease, to information encoded in the genome and in molecular networks, including via multiscale epigenetic mechanisms that interact with physical processes in the physiological environment.

To address this challenge, the Physiome Project is developing an integrated biophysically-based modelling framework with associated modelling standards and a model repository in order to provide mechanistic, anatomically based, multiscale models of physiological function to help in the interpretation of complex physiological data.

The concept of a “Physiome Project” was presented in a report from the Commission on Bioengineering in Physiology to the IUPS Council at the 32nd World Congress in Glasgow in 1993. The term “physiome” comes from “physio” (life) + “ome” (as a whole), and is intended to provide a “quantitative description of physiological dynamics and functional behaviour of the intact organism”. A satellite workshop “On designing the Physiome Project”, organized and chaired by the Chair of the IUPS ‘Commission on Bioengineering in Physiology’ (Jim Bassingthwaighte), was held in Petrodvoretz, Russia, following the 33rd World Congress in St Petersburg in 1997. A synthesium on the Physiome Project was held at the 34th World Congress of IUPS in Christchurch, New Zealand, in August 2001 and the Physiome Project was designated by the IUPS executive as a major focus for IUPS during the next decade. Peter Hunter was appointed Chair of the newly created Physiome Commission of the IUPS in 2000. The current chair of the renamed ‘Physiome and Bioengineering’ Committee is Andrew McCulloch.

The Physiome and Systems Biology Committee

The Committee promotes Physiome and Systems biology as an integral part of modern physiology. It is is chaired by Andrew McCulloch (USA)

Members of the committee are Jim Bassingthwaighte (USA), Colleen Clancy (USA), Andrew Greene (USA), Peter Hunter (New Zealand), Virginia Huxley (USA), Fumihiko Kajiya (Japan), Richard Kitney (UK), Nigel Lovell (Australia), Rossana Occhipinti (USA), Stig Omholt (Norway), Aleksander Popel (USA), Axel Pries (Germany), Rod Smallwood (UK) and Hans V.Westerhoff (Netherlands)

Physiome modelling standards and Physiome Model Repository (PMR)

Building a comprehensive model of human physiology requires contributions from many groups but the majority of published biological models are, unfortunately, not reproducible. Even in cases where authors make their model code available on a website, the code usually does not match the equations presented in the paper and the model results shown in graphical form are not reproducible without substantial effort, since the models are published with missing or incorrect values for some parameters. Since the Physiome Project was initiated over twenty years ago, several markup languages have been developed to address this problem: CellML, SBML and NeuroML for encoding the syntax and semantics of model descriptions, and SED-ML for encoding the model simulation itself.

The Physiome Model Repository and BioModels database have been established to store physiological models encoded in these standards. Between them PMR and BioModels now contain over 2000 models, with both databases being widely used and recommended by many journals.