BioDynaMo 1.04

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)

BioDynaMo 1.02

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

BioDynaMo 1.0

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

Initial BioDynaMo Release

Fix cmake config error

Snap package config file was generated before install path was
modified