Journal article published and more on this week’s OpenWorm round-up!

We’re happy to announce an OpenWorm perspectives article was recently published in “Frontiers in Computational Neuroscience.” Congratulations and many thanks to the authors and contributors! Read the article here.

Check out the latest developments in OpenWorm from our biweekly meeting:

GITHUB

Highlighted Activities

dkruchinin forked openworm/org.geppetto.testbackend to dkruchinin/org.geppetto.testbackend
Oct 9

slarson created branch tests at openworm/muscle_model
Oct 8

samuelgunadi forked openworm/OpenWorm to samuelgunadi/OpenWorm
Oct 8

GOOGLE GROUPS

OpenWorm perspectives article published in Frontiers in Comp. Neuro.
By Stephen, 2 posts 3 views
Oct 11

Re: [openworm-discuss] Digest for openworm…@googlegroups.com - 5 updates in 2 topics
By Miguel Camarena, 2 posts 4 views
Oct 9

Fwd: [Neuroinfo] New release of NeuroML 2 and LEMS and two recent publications
By Stephen, 1 post 4 views
Oct 6

Read more at:

6c elegans, neuroscience, open science, neurons,

OpenWorm weekly round-up!

Geppetto 0.1.7 released and more on the OpenWorm weekly round-up!

Geppetto 0.1.7 was released in the past few days and can be found here. This release includes several performance improvements, new widgets to explore the content of the simulation, an improved console and many bug fixes. The live deployment of Geppetto can be accessed at http://live.geppetto.org.

Check out the latest developments in OpenWorm from our biweekly meeting:

GITHUB

Highlighted Activities

mlolson created branch wormsim at openworm/org.wormsim.frontend
Sept 26

mlolson created branch wormsim at openworm/org.geppetto
Sept 26

dkruchinin forked openworm/org.geppetto.frontend to dkruchinin/org.geppetto.frontend
Sept 26

skhayrulin forked openworm/org.geppetto.solver.sph to skhayrulin/org.geppetto.solver.sph
Sept 25

skhayrulin created branch membranePorting_issue255 at openworm/org.geppetto.solver.sph
Sept 25

albi3ro forked openworm/OpenWorm to albi3ro/OpenWorm
Sept 24

GOOGLE GROUPS

Geppetto build problem
By Dan Kruchinin, 2 posts 11 views
Sep 26

Just loaded 600+ mb to the Google Drive
By Michael Currie, 1 post 2 views
Sep 25

Visualization of biological neural network
By Matt Olson, 3 posts 17 views
Sep 25

movement_validation bulletin
By Michael Currie, 4 posts 18 views
Sep 24

Read more at:

TWITTER

Gary Marcus @GaryMarcus
Sep 27
Emulate a fruit fly brain on your own GPU! #opensource @openscience @openworm http://neurokernel.github.io/

Read more at: https://twitter.com/OpenWorm

6neuron, Neuroscience, open science, c elegans,

OpenWorm weekly round-up!

DevoWorm, status update and more OpenWorm weekly round-up!

Watch the newest Journal Club, DevoWorm - Raising the Worm, to learn about this exciting subproject within OpenWorm which seeks to simulate the cell-by-cell divisions and growth that leads to the adult. .

Check out the latest developments in OpenWorm from our biweekly meeting:

GITHUB

Highlighted Activities

adrianq created branch modelpopulation at openworm/org.geppetto.samples
Sept 14

crf1111 forked openworm/OpenWorm to crf1111/OpenWorm
Sept 12

tarelli created branch adrianq-neuromlWidget at openworm/org.geppetto.frontend
Sept 11

portegys pushed to master at openworm/bionet
Sept 9

borismarin created branch generalize_onStateChange_callbacks at openworm/org.geppetto.frontend
Sept 8

GOOGLE GROUPS

Multiple NeuroML2 modeling issues cropping up in OpenWorm
By Stephen, 3 posts 3 views
Sep 12

Re: CyberElegans on Linux/Mac
By Stephen, 2 posts 14 views
Sep 11

Read more at:

TWITTER

OpenWorm @OpenWorm
Sep 12
#OpenWorm journal club: “DevoWorm - Raising the worm” is LIVE - https://www.youtube.com/watch?feature=player_embedded&v=XRm7SxTpmQo …

J. Pablo Fernández @pupeno
Sep 12
There’s a worm in my apple! But it’s fine because it’s an @openworm! pic.twitter.com/Kiz9QhPC2h

Orion Bionetworks @OrionBionetwork
Sep 11
Save the date 9/30, noon-1p EDT FREE Webinar on bioinformatics! https://plus.google.com/u/0/events/cc6tc32hevji94007c0pf3u5c4s … pic.twitter.com/TalwAcQe3j

OpenWorm @OpenWorm
Sep 11

What the humble worm might tell us about doubling our lifespan - http://theconversation.com/what-the-humble-worm-might-tell-us-about-doubling-our-lifespan-31481 …

OpenWorm @OpenWorm
Sep 10
#openworm bi-weekly status update is LIVE! - http://youtu.be/VO12yvwk08s

Read more at: https://twitter.com/OpenWorm

6open science, c elegans, Neuroscience,

New status update and more OpenWorm weekly round-up!

Check out the latest developments in OpenWorm from our biweekly meeting

GITHUB

New Issues This Week

Issues Updated This Week

Issues Closed This Week

GOOGLE GROUPS

Re: simulating worm on local system
By Stephen, 1 post 4 views
Aug 29

Who’s an advanced math wizard?
By Stephen, 1 post 3 views
Aug 29

SciUnit: getting operational
By Stephen, 7 posts 36 views
Aug 29

Read more at:

TWITTER

OpenWorm @OpenWorm
Aug 30
#openworm swag sightings in the wild are on the rise! pic.twitter.com/LLD5UT5lyP

OpenWorm @OpenWorm
Aug 30
Thanks all for help finding a #math expert — we got a volunteer! Stay tuned for an #openworm journal club on it soon! #openscience

OpenWorm @OpenWorm
Aug 29
Any #math wizards out there who could help? Thanks! http://blog.openworm.org/post/96090226275/any-advanced-math-wizards-out-there … #openscience

Read more at: https://twitter.com/OpenWorm

6Neuroscience, c elegans, open science,

Any advanced math wizards out there?

Update #1: Some people asked why we are interested in this. It has applications to complexity science— basically you can look at a nervous system (or any complex biological system) as a high-dimensional non-linear dynamical system.  The dissertation is exploring the mathematical properties of such a dynamical system, so the methods in the thesis could potentially be turned into a better way to understand what the nervous system (or any biological system) is doing.

Update #2: We got a volunteer!!  Thanks to all who shared this around.  Stay tuned for an OpenWorm journal club on this subject soon!

Hi all,

  Does anybody out there understand the following advanced math ideas well and would be willing to explain them to the rest of us?
  • diffeomorphism
  • Riemannian manifold
  • tangent bundle
   Further, who here looks at this definition and it makes sense to them?
image
   If that’s you, we could really use you to get on a hangout and explain the following dissertation to the rest of us mere mortals.  If you or someone you know would be willing to do that, it would be AWESOME.  This kind of math (and this dissertation in particular)  is actually extremely relevant to what we are doing here but out of reach at the moment.
   Let us know via any of the regular channels.  Thanks!!

6openworm, math, advanced math, help,

OpenWorm weekly round-up!

GITHUB

New Issues This Week

Issues Updated This Week

Issues Closed This Week

GOOGLE GROUPS

SciUnit: getting operational
By Stephen, 6 posts 31 views
Aug 22

c302 questions
By Tom Portegys, 16 posts 82 views
Aug 20

Statistical measures within SegWorm code base
By Stephen, 2 posts 16 views
Aug 20

Geppetto 0.1.6 released
By Matteo Cantarelli, 1 post 10 views
Aug 19

Re: [openworm-discuss] Genohacking C. elegans
By Stephen 7 posts 30 views
Aug 19

Read more at:

6c elegans, Neuroscience, neuron, open science,

Geppetto 0.1.6, Journal Club & more on this week’s OpenWorm round-up!

Geppetto release 0.1.6 is now live and can be found here for download. Want more updates on Geppetto? Get the latest Geppetto biweekly meeting minutes.

Interesting in learning about the scientific method 2.0? Watch the OpenWorm Journal Club to find out.

Check out the latest developments in OpenWorm from our biweekly meeting

BLOG

Connectomes Big and Small
Aug 11st 2014, 9:24 am
Guest blog: Lav R. Varshney I have been following the OpenWorm project with great interest over the last year and am really …

GITHUB

New Issues This Week

Issues Updated This Week

Issues Closed This Week

GOOGLE GROUPS

Re: [openworm-discuss] Genohacking C. elegans
By Stephen, 6 posts 17 views
Aug 17

Visualizing data using d3js
By Ashish Kadam, 4 posts 34 views
Aug 17

SciUnit: getting operational
By Stephen, 4 posts 11 views
Aug 15

Stanford Light Field Microscope Project
By John Ballentine, 2 posts 17 views
Aug 14

Openworm engineering blog
By Matt Olson, 4 posts 12 views
Aug 14

general meeting
By Joe Landau, 2 posts 10 views
Aug 13

Wanted: NEURON and Brian recordings
By Johannes Rieke, 4 posts 21 views
Aug 10

Read more at:

TWITTER

OpenWorm @OpenWorm
Aug 15
OpenWorm Journal Club is Live! https://plus.google.com/b/117948341754627144949/events/c4s7e1g676dgl909r8819oklcso … Scientific Method 2.0

OpenWorm @OpenWorm
Aug 13
Not a worm muscle but neat anyhow! http://i.imgur.com/fgRP0H7.gif

OpenWorm @OpenWorm
Aug 13
#openworm status update is LIVE - http://youtu.be/bkwFTyRxHXU

Royal Irish Academy @RIAdawson
Aug 12
Letter from Crick and Watson to Erwin Schrodinger dated 12 Aug 1953 re: What is Life? & the impact on their careers pic.twitter.com/egMBNcUyR5

Read more at: https://twitter.com/OpenWorm

6open science, neuron, c elegans, Neuroscience,

Connectomes Big and Small

Guest blog: Lav R. Varshney

I have been following the OpenWorm project with great interest over the last year and am really glad to be contributing to it through some blog posts on mathematical theories of neurobiology and related subjects.  As background, I am an assistant professor of electrical and computer engineering at the University of Illinois at Urbana-Champaign, where my research focuses on information in complex systems, whether neurobiological, sociotechnical, or nanoscale.  In the past, my colleagues and I had worked on completing and analyzing the hermaphrodite C. elegans connectome in a paper, whose data is now being used in OpenWorm.  This built on the pioneering work of John White, et al.

An opening line of our paper said that “the wiring diagram reported here can further be used to generate predictions about signal propagation in future perturbation, ablation, or artificial stimulation experiments” but what really intrigues me these days is the possibility of computational simulation experiments that yield a detailed, principled understanding of C. elegans biology.  This, of course, is the promise of the OpenWorm project.

Read More

6openworm, connectome, neurons,

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