SUPR
pbdMPI-testing
Dnr:

NAISS 2024/22-1206

Type:

NAISS Small Compute

Principal Investigator:

Andrei Kramer

Affiliation:

Kungliga Tekniska högskolan

Start Date:

2024-09-25

End Date:

2025-10-01

Primary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Allocation

Abstract

Our work is organized within the Brain-IT Multidisciplinary collaboration programme (MCP) of the Swedish e-science research center (SeRC): https://e-science.se/people-and-research/mcps/mcp-brain-it/ Part of this program is the development of an R package (uqsa), which helps with parameter estimation of biological models. This package uses several other packages that we developed, as summarized on this github repository: github.com/icpm-kth: 1. icpm-kth/SBtabVFGEN 2. icpm-kth/RPN-derivative 3. icpm-kth/rgsl These packages (1) parse systems biology specific files (SBtab files) and create Ordinary Differential Equation models (ODE) based on the reactions described in the files, (2) automatically generate C code for the vector field, with analytic Jacobians, and (3) provide an R interface to ODE solvers in the GNU scientific library (C code) which use the auto-generated model code in the form of a shared library (dynamically loaded). Using these helper packages, uqsa performs a parallel tempering Markov chain Monte Carlo sampling of the model parameters. The implementation currently uses the pbdMPI package (an R package) -- works on our local workstations. Until now, this package was not installable on Dardel. Very recently, PDC support has found a workaround that successfully installs this missing package. The small NAISS allocation we apply for has the purpose of testing this workaround installation on the actual uqsa package rather than pbdMPI supplied test scripts. We will use the model of vesicular fusogenicity (unpublished work in progress) that Brain-IT is currently developing with Ranjita Dutta Roy. If these tests arfe successful, we will persue this project within a medium allocation.