Biodynamo Versions Save

BioDynaMo is a high-performance and modular, agent-based simulation platform.

v1.04

1 year ago

The following people have contributed to this version (ordered by the number of contributions):

  • Lukas Breitwieser
  • Tobias Duswald
  • Nicolò Cogno
  • Fons Rademakers
  • Ahmad Hesam
  • Jack Jennings
  • Moritz Grabmann

New Features and Improvements

  • Add check for PVSM output files to system tests #280
  • Generalize continuum integration #260
  • Improve scheduler information #277
  • Update flocking demo with local fluctuations #256
  • Added check for decay rate in diffusion grid #271
  • Make floating-point precision adjustable #253
  • Improve UniformGridEnvironment::Box::Iterator interface
  • Add switch to turn off automatic sim size detection in UniformGridEnvironment
  • Add missing ForEachNeighbor implementation for UniformGridEnvironment
  • Add BinarySearch.DuplicatesLarge test
  • Remove const specifier from Agent::RemoveFromSimulation
  • Improve the time series collection API #266
  • AgentPointer return nullptr directly for corresponding AgentUid
  • Make InPlaceExecutionContext::remove_ protected
  • Make Agent::RemoveFromSimulation virtual
  • Remove all virtual functions from InlineVector
  • Introduce different AgentPointer modes #264
  • Improve mechanism to reuse the index part of AgentUids #263
  • Update paraview build on macOS i386 #261
  • Don't run Singularity GHA on all branches
  • Avoid parsing of bdm.json with bdm test
  • Add macOS packages to user guide
  • Extend DiffusionGrid interface for full gradient information #257
  • Link Singularity in User Guide
  • Add left-multiplication to MathArray #255
  • Minor code quality improvements #252
  • Create BioDynaMo singularity image #244
  • Reenable gitpod image workflow but only for manual triggering
  • Add additional LamdaFunctor tests
  • Add safety check in function PlotNeighborMemoryHistogram
  • Improve documentation of Agent::RemoveBehavior
  • Add coverage reporting with SonarCloud #247
  • Upgrade to ParaView 5.10 on macOS #235
  • Update continuum models #241
  • Add improvements suggested by Sonar Cloud #246
  • Add quality checks with Sonar Cloud #245
  • Add SWC export for neurons #243
  • Update link to endpoint package (CentOS CI)
  • Add CLI wrapper for bdm-config #238
  • Add ProgressBar to visualise progress in Simulate() #237
  • Remove benchmark from default build target #236
  • Add SHA's for macOS 12.1 and Ubuntu 22.04.
  • Extend functionality of show_simulation_step parameter #234

Bug Fixes

  • Fix issue with markupsafe which breaks nbconvert and thus the website #281
  • Fix Python libraries on macOS #279
  • Fix warning in multi-simulation mode #272
  • Update GHA for macOS and fix notebooks on Ubuntu #274
  • Fix notebook related packages on CentOS #275
  • Fix issues introduced due to the global edit from double to real_t in OpenCL code.
  • Fix to find python3.9 on macOS.
  • Added version check and threshold fix for ParaView in epidemiology demo
  • Attribute environment update time to the correct operation
  • Reduce size of UniformGridEnvironment::Box
  • Remove obsolete parameter from toml file
  • Fix NUMA bug in ResourceManager::RemoveAgents
  • Fix GHA copyright script for linux
  • Fix DiffuseWithOpenEdge #248
  • Add fixes for code-smells #249
  • Fix bug in function GenerateSimulationInfoJson
  • Add additional AgentPointer tests; fix bug in AgentPointer
  • Fix possible race condition in user-defined thread-safety mechanism #262
  • Fix normalization of the diffusion gradient #259
  • Fix static agents bug in mechanical_forces_op
  • Fix compiler warnings #254
  • Fix date-format in userguide/Singularity.md

Examples

New Demos

  • Cell monolayer growth #278
  • Flocking Demo #240

Supported Platforms

  • Ubuntu 18.04, 20.04
  • CentOS 7
  • MacOS 11.7 and 12.6 (Intel and ARM)

v1.02

2 years ago

The following people have contributed to this version (ordered by the number of contributions):

  • Lukas Breitwieser
  • Tobias Duswald
  • Fons Rademakers
  • Ahmad Hesam
  • Will Hemsley

New Features

  • Enabled one-line install script to install arbitrary BioDynaMo versions #231
  • Add Scheduler function to print operation information
  • Added parallelized optimization manager #205
  • Added googletest support for simulations #187
  • Improved biodynamo cli #215
  • Added experimental version of the automated benchmarking suite #202
  • Added CopyExecutionContext
  • Added support for different execution orders
  • Introduced execution context interface #189
  • Reduced memory consumption of the BDM memory manager #186
  • Added SphericalAgent
  • Added toroidal space boundary condition
  • Added RandomizedRm to randomize the iteration over all agents
  • Added support for hierarchical agent-based models
  • Added analysis classes to simplify data collection and plotting #177
  • Improved random number generation
  • Added Scheduler::SimulateUntil(exit_condition)
  • Added class LambdaFunctor and function L2F to simplify functor creation #175
  • Added octree and kd-tree as alternative environments #169

Bug Fixes

  • Fixed environment inconsistencies #226
  • Added simulation dependent diffusion time step #198
  • Fixed bug in diffusion grid initialization #199
  • Fixed MathArray::Norm and Normalize for zero vector #194
  • Do not call Rm::EndOfIteration in ExecCtxt::SetupIterationAll
  • Fixed errors in the static agent detection mechanism #191
  • Fixed race condition in DiffusionGrid::ChangeConcentrationBy
  • Changed BioDynaMo version from vXX.YY-ZZ-gSHA to vXX.YY.ZZ-SHA #216

Examples

New Demos

  • Binding cells
  • Pyramidal cell growth

New Notebooks

  • ST01-model-initializer.ipynb
  • ST02-user-defined-random-number-distribution.ipynb
  • ST03-agent-reproduction-mortality.ipynb
  • ST04-agent-reproduction-with-behaviors.ipynb
  • ST05-agent-reproduction-advanced.ipynb
  • ST06-environment-search.ipynb
  • ST07-multi-scale-simulation.ipynb
  • ST08-histograms.ipynb
  • ST09-timeseries-plotting-basic.ipynb
  • ST10-timeseries-plotting-and-analysis.ipynb
  • ST11-multiple-experiments-statistical-analysis.ipynb
  • ST12-hierarchical-model.ipynb
  • ST13-dynamic-scheduling.ipynb
  • ST14-randomize-iteration-order.ipynb
  • ST15-replace-interaction-force.ipynb

Supported Platforms

  • Ubuntu 18.04, 20.04
  • CentOS 7
  • macOS 10.15, >=11.6 and >=12.0

v1.0

3 years ago

The following people have contributed to this first major version (ordered by number of contributions):

  • Lukas Breitwieser
  • Ahmad Hesam
  • Fons Rademakers
  • Konstantinos Kanellis
  • Jean de Montigny
  • Roman Bauer
  • Giovanni De Toni
  • Jack Jennings
  • Dorukhan Arslan
  • Nam Nguyen
  • Johannes Franz
  • Lukasz Stempniewicz
  • Robert Harakaly
  • Sadyksaj
  • Tobias Duswald
  • Victor Drobny

Main features

  • A general API to implement and customize agent-based models
  • A fully parallelized, high-performance simulation engine
  • Ability to offload computations to GPUs of all major vendors
  • Large-scale model support. BioDynaMo can simulate billions of agents on a single server.
  • Predefined building blocks for simulations in neuroscience, oncology, and epidemiology
  • Support for spherical and cylindrical agent geometries
  • Diffusion methods: Euler, Runge-Kutta
  • Multi-scale simulation support
  • Visualization in ParaView
  • Parameter configuration: JSON, C++ interpreter script, command line, or in-code
  • Automatic backup and restore functionality using ROOT
  • BioDynaMo Notebooks for rapid web-based prototyping

For a more detailed description of BioDynaMo's features and capabilities, please have a look at the following publication:

BioDynaMo: a general platform for scalable agent-based simulation Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer bioRxiv 2020.06.08.139949; doi: https://doi.org/10.1101/2020.06.08.139949

Demos

BioDynaMo v1.0 comes with the following demos:

  • Cell division
  • Diffusion
  • Soma clustering
  • Tumor concept
  • Epidemiology
  • Gene regulation
  • Parameters
  • Multiple simulations
  • Makefile project

Supported Platforms

  • Ubuntu 18.04, 20.04
  • CentOS 7
  • macOS 10.15 and macOS 11.1

v0.1.0

6 years ago