List view
- Due by July 30, 2021•2/2 issues closed
Some additions to the 0.9 release
Due by September 30, 2020•5/5 issues closed- No due date•7/7 issues closed
Next release of OpenWorm Stack. To potentially contain: * Pointers to authoritative repos with released versions * Geppetto incorporated * PyOpenWorm-based generation of CElegansNeuroML data incorporated
Due by February 26, 2018•5/5 issues closed- Due by December 20, 2017•3/3 issues closed
- No due date•3/3 issues closed
Points discussed include: * Presenting an OpenWorm journal club on the recent stochastic neuronal model - Education Committee * Synchronize with the larger OpenWorm roadmap * Take the start of the c302-Sibernetic bridge and make it runnable and improve correctness (sibernetic) * Improving neuronal model (c302) * Improving synapse model (c302) * Improving understanding of the whole nervous system circuit (neuronal-analysis) Aiming to have the TU Wien team able to implement one new circuit in c302 by end of November 2016
No due date•6/6 issues closedThis milestone seeks to improve the performance of Sibernetic so it can be run in a reasonable amount of time on a PC. More information about the Sibernetic project can be [found on the documentation page](http://docs.openworm.org/en/latest/Projects/sibernetic/)
No due date•5/5 issues closedIn the past releases we created a [database](http://docs.openworm.org/en/0.5/resources.html#openworm-database) of information about the c. elegans. Separately from this we [created scripts that read spreadsheets](https://github.com/openworm/CElegansNeuroML/blob/master/CElegans/pythonScripts/RegenerateConnectome.py) in order to produce model files like the NeuroML connectome. This story is to create a single code base that can both serve as a means for an ever improving repository of data, and an automated way to produce model files for the simulation based on that data. Some principles to follow: * There should be a one stop shop for accessing the data that goes into the model * Model files (e.g. NeuroML) should be able to be easily updated as new information / data are integrated * Data that are incorporated into the model should have references back to the source of that data. Currently the candidate codebase for this pipeline is the new [PyOpenWorm library](https://github.com/openworm/PyOpenWorm). More information about the data representation project [can be found in the documentation](http://docs.openworm.org/en/latest/Projects/datarep/)
No due date•18/18 issues closedCurrently the Sibernetic code base does not output any sensory feedback into neurons. However, there is a [Python layer](https://github.com/openworm/Smoothed-Particle-Hydrodynamics/blob/master/src/main_sim.py) that implements muscle activations. This story is to enable mechanosensory feedback coming from the model into the Python layer so it can be integrated into a model of 302 neurons. This means when the skin of the worm body is touched or, more generally, deformed, a signal can be received into a neuron. More information about the Sibernetic code is [found in the documentation](http://docs.openworm.org/en/latest/Projects/sibernetic/)
No due date•1/1 issues closedIn the current Sibernetic code base, the muscles are activated by [simple sine functions](https://github.com/openworm/Smoothed-Particle-Hydrodynamics/blob/master/src/main_sim.py#L25). This story aims to replace these with a model of 302 neurons activating the muscles. This does not need to be fully accurate, it just needs to have the code elements in place to perform this task. Tuning and improving accuracy of the model will come in a further story. While the ideal model would be the full multi-compartmental model from the [CElegansNeuroML project](http://docs.openworm.org/en/latest/Projects/datarep/#neuroml-connectome), this story can be satisfied with a simpler model of the 302 neurons so long as it works. More information about this project [can be found in the documentation](http://docs.openworm.org/en/latest/Projects/sibernetic/)
No due date•1/1 issues closedAs a user, I want to see the [proof of concept sibernetic worm](https://github.com/openworm/OpenWorm/issues?milestone=20) in my web browser so that anyone around the world can play with it. Practically, this means porting the proof of concept scene into Geppetto. More information about the Geppetto project can be [found in the documentation](http://docs.openworm.org/en/latest/Projects/geppetto/)
No due date•4/4 issues closedAs a scientist or developer, I want to be able to run a program and see a wiggling worm in 3D in front of me. This refers to having a running simulation with the following components: * Four rows of 'elastic matter muscles' fixed in a 'elastic matter shell' * 'Elastic matter shell' is filled with liquid that puts outward pressure on shell * 'Elastic matter muscles' put force on 'elastic matter shell' * Simple sinusoidal input (no neurons) can be applied to 'elastic matter muscles' to produce simple 'wiggling'. To get rapidly to the end goal, this implementation will be done with some combination of Sibernetic + Configuration Generator + Python scripts. A Geppetto implementation will come later. This story breaks down [the epic to predict behavior from the WormBehavior database](https://github.com/openworm/OpenWorm/issues?milestone=22)
Due by December 31, 2013•3/3 issues closedAs a scientist or developer, I want to be able to run a test suite against the simulation that will show me how close the model is to real data. In order for a model to demonstrate scientific value, it has to make falsifiable predictions. The target data to be able to predict will be drawn from the [WormBehavior database](https://www.dropbox.com/s/tqr3abcrr8dt3bi/A%20database%20of%20Caenorhabditis%20elegans%20behavioral%20phenotypes.%20-%20Yemini%20et%20al.%20-%202013.pdf). This milestone will involve working with these data, creating a code base that can compare movement output from the simulation with ground truth from the database and produce an accuracy score. More information about this story can be found [on its project page in the documentation](http://docs.openworm.org/en/latest/Projects/worm-movement/) This story breaks down [the epic to predict behavior from the WormBehavior database](https://github.com/openworm/OpenWorm/issues?milestone=22)
No due date•7/7 issues closedCode has been ported from [the original C++ host](https://github.com/openworm/Smoothed-Particle-Hydrodynamics) to a Java host in the form of [a Geppetto plugin for fluid mechanics](https://github.com/openworm/org.geppetto.solver.sph). This milestone is about making sure that the 2 versions behave the same and given the same initial conditions give the same results. @gidili is taking the lead on this with help from @skhayrulin and @tarelli
Due by July 31, 2013•6/6 issues closedWe are writing a manuscript focusing on the work we have to implement SPH in the project and apply it to muscle cells and the worm body. @vellamike, @a-palyanov and @skhayrulin are taking the lead on this, The proposal is to do this after [the Sibernetic proof of concept worm wiggling is complete](https://github.com/openworm/OpenWorm/issues?milestone=20&state=open).
Due by December 17, 2013•5/5 issues closedWe have received a contribution of movies from the Leifer lab recording from real neurons in real worms. We will extract calcium signals from these movies and use them to tune parameters in our NeuroML connectome model. @shamdor will take the lead on this.
Due by June 1, 2013•1/1 issues closedThe NeuroML connectome model at https://github.com/openworm/CElegansNeuroML requires a number of updates before it can be used for multicompartmental simulations. Padraig Gleeson will take the lead on this.
No due date•2/2 issues closedThis milestone is to track porting of the fluid mechanics solver to Geppetto. Responsible for this delivery is Giovanni Idili. <!--- @huboard:{"status":"wip","order":4.5} -->
Due by June 30, 2013•12/12 issues closedWe will show that we have built a model of C. elegans muscle cell that matches data recorded from the nematode muscle cell. In part, we will use techniques of model optimization to fill in gaps in the model parameter space (deduce unmeasured parameters). The main technical challenge is tuning muscle cell passive properties and building a larger data set (more cell recordings). @vellamike is taking the lead on this.
No due date•2/2 issues closedWe will ensure that the software that we are producing can be executed by others outside the project and that there is clear documentation explaining how to install and use it. Stephen Larson will take the lead on this.
Due by June 4, 2013•3/3 issues closedWe will drive people to help mark the synapses of the c. elegans using real electron micrographs taken from the tissue of the worm. We will incorporate these positions into the NeuroML connectome. Stephen Larson will take the lead on this.
Due by June 4, 2013•1/1 issues closedWe will update the website with additional information to make the project more friendly to outside onlookers. Matteo Cantarelli (@tarelli) will take the lead on this.
Due by February 26, 2013•2/2 issues closedWe'll submit a perspectives paper giving an overview of the project to a journal for publication. Balazs Szigeti will take the lead on this. <!--- @huboard:{"status":"wip","order":3.5} -->
Due by June 4, 2013•8/8 issues closedThe c. elegans is a complex organism and has a complex array of data that surround it. We will produce visualizations and infographics that help new users to understand what kind of data exist and where the gaps are for building a more detailed model. Stephen Larson will take the lead on this.
Due by June 4, 2013•2/2 issues closedGood models of ion channels are crucial to have an increasingly accurate representation of the dynamics of neurons and other cells in the c. elegans. A detailed database will be created and as much as possible we will create ChannelML models of each ion channel. Neuropeptides drive c. elegans behavior in a significant way. We will aggregate what is known about the c. elegans neuropeptides and the receptors they act on in a database. Tim Busbice will take the lead on this.Tim Busbice will take the lead on this.
Due by June 4, 2013•1/1 issues closedGeppetto is the Systems Biology Open Simulation Platform developed as part of the OpenWorm project and formerly known as "Simulation Engine". Geppetto is a plugin-based engine, which serves as core platform to have computational algorithms and elements intersect. Geppetto's frontend is a web-based 3D visualization engine which allows rendering the algorithms running and outside users to interact with the model. Being Geppetto a modular platform individual functionalities are provided by individual plugins. Separate milestones are tracking the development of Geppetto plugins to allow solving of multi-compartmental neuronal models and fluid mechanics simulations. This milestone is to track packaging of Geppetto so that it can be distributed, deployed and used easily. Also through this milestone we'll track all the issue related to interoperability of the different plugins and necessary platform support to allow their development. Matteo Cantarelli (@tarelli) is taking the lead on this. <!--- @huboard:{"status":"wip","order":2.5} -->
Due by June 4, 2013•8/8 issues closedBuilding on the neuronal simulator in the current simulation engine, the functionality will be extended to efficiently solve large numbers of multi-compartmental models of neurons. Giovanni Idili is taking the lead on this.
Due by June 4, 2013•3/3 issues closedImprovements to the mechanics engine that implements smoothed particle hydrodynamics (SPH). Andrey Palyanov is taking the lead on this.
Due by June 4, 2013•6/6 issues closedThis milestone builds on earlier work with the muscle cell model to create a bi-directional connection between a mechanical model of the muscle and an electrical model of the membrane electrophysiology. The integrated model combines both a discrete particle representation using a smoothed particle hydrodynamics algorithm and a conductance-based representation of electrophysiology using the hodgkin-huxley equations. Mike Vella is taking the lead on this.
Due by June 4, 2013•3/3 issues closed