New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add cell lineage info to PyOpenWorm #7

Closed
slarson opened this Issue May 13, 2014 · 14 comments

Comments

Projects
None yet
4 participants
@slarson
Member

slarson commented May 13, 2014

Cell lineage refers to the tree of cell divisions that occurs when an organism is growing from an embryo. We'd like to have a data structure that captures this for c. elegans. The data are out there -- now we'd like to put them into PyOpenWorm.

This is the first step in a greater project to be able to render lineage trees as "differentiation trees" for exploration and potentially simulation down the road.

  • Identify best data source to begin working with
  • Write a simple python script that pulls out the names of the cells and the cell division relationships and displays to console
  • Augment the script to dump the data into the PyOpenWorm SQLite3 DB.
  • Augment PyOpenWorm to pull this data out from the SQLite3 DB and construct an RDF graph out of it
  • Build accessor functions in PyOpenWorm that can pull the whole lineage into a networkX graph, and also can report lineage information when asked for a specific cell.

Original issue: openworm/OpenWorm#179

@slarson slarson added the enhancement label May 13, 2014

@slarson slarson referenced this issue May 13, 2014

Closed

Add cell lineage info to PyOpenWorm #179

0 of 5 tasks complete
@balicea

This comment has been minimized.

balicea commented May 13, 2014

UPDATE (5/13):

I have established my own Github repository for the DevoWorm project here (nuts and bolts issues, Python code, etc:
https://github.com/balicea/DevoWorm

I also have an extracted dataset that I have been playing with:
https://drive.google.com/file/d/0B7RsqJbITXXAM0RJQmkzb1o4U1E/edit?usp=sharing

@DickGordonCan

This comment has been minimized.

DickGordonCan commented May 29, 2014

For background on differentiation trees see:
Gordon, R. (1999). The Hierarchical Genome and Differentiation Waves: Novel Unification of Development, Genetics and Evolution. Singapore & London, World Scientific & Imperial College Press. http://www.worldscientific.com/worldscibooks/10.1142/2755
For C. elegans, we have the cell lineage tree:
Sulston, J.E., E. Schierenberg, J.G. White & J.N. Thomson (1983). The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100(1), 64-119.
The left/right organization of this tree is according to which cell was the anterior/posterior cell after a cell division. For the asymmetric divisions, which are the majority in C. elegans, we need to reorder the tree per small/large cell to create the C.elegans differentiation tree.

@DickGordonCan

This comment has been minimized.

DickGordonCan commented May 29, 2014

Note:
Karabey, Y. (2003). Corrections to: The embryonic cell lineage of the nematode Caenorhabditis elegans. http://www.wormatlas.org/ver1/Sulstonemblin_1983/toc.html

@balicea

This comment has been minimized.

balicea commented May 30, 2014

An update on the white paper and dataset. I have posted version 2.0 of both:

White Paper, 2.0 (added more detail, especially reflecting our last meeting):
http://figshare.com/articles/From_Differentiation_Waves_to_Wriggling_new_views_on_C_elegans_development/1015760

Dataset, 2.0 (cleaned up tabbed pages and extracted lineage information from the cell names):
http://figshare.com/articles/DevoWorm_Dataset/1040317

Any questions, let me know. Bradly Alicea

@balicea

This comment has been minimized.

balicea commented Jun 4, 2014

I posted a project announcement/advertisement to my blog Synthetic Daisies (Now Announcing the DevoWorm Project). The blog has a modest biology/computational readership. Check it out:

http://syntheticdaisies.blogspot.com/2014/06/now-announcing-devoworm-project.html

@mwatts15

This comment has been minimized.

Contributor

mwatts15 commented Jun 6, 2014

This is a list of names which I wasn't able to resolve immediately: http://pastebin.com/biQ8dZuQ
I'll be looking at the associate wormbase entries to try to resolve them.

@balicea

This comment has been minimized.

balicea commented Jun 6, 2014

Mark,

  Thanks. I'll make a record of them (store them in my data files). 

I do not know what their identity is.

Bradly Alicea

On 6/6/2014 9:19 AM, mwatts15 wrote:

This is a list of names which I wasn't able to resolve immediately:
http://pastebin.com/biQ8dZuQ
I'll be looking at the associate wormbase entries to try to resolve them.


Reply to this email directly or view it on GitHub
#7 (comment).

@mwatts15

This comment has been minimized.

Contributor

mwatts15 commented Jun 6, 2014

Recovered what looks like the source from wormatlas. Explains to me the '.' versus ' '.

@mwatts15

This comment has been minimized.

Contributor

mwatts15 commented Jun 7, 2014

I'm still fuzzy on where the P cells originate from. The 'cytoscape' spreadsheet has slashes in the names of P cells:
ABplapaapp (P1/2 L) P1/2 L
ABplapapaa
ABplapapap (P9/10 L) P9/10 L
ABplapappa (P11/12 L) P11/12 L
ABplapappp
ABplappaaa (P3/4 L) P3/4 L
ABplappaap (P5/6 L) P5/6 L

In wormbase, these relationships are shown by Equivalence_fate and its inverse Equivalence_origin, but the semantics on this are unclear to me.

@balicea

This comment has been minimized.

balicea commented Jun 9, 2014

Steve McGrew's ALFRED proposal and Bradly Alicea's literature search on developmental evolutionary algorithms:

https://www.dropbox.com/sh/iir0h6l8l4f6tbw/AACbWTivw62AyRcSK5UPXvYia

@slarson

This comment has been minimized.

Member

slarson commented Jun 20, 2014

@mwatts15 for names like "ABplapapap (P9/10 L) P9/10 L", the first string with no spaces is the developmental name and the name in parens with slashes are the non "lineage" naming scheme. You can see an example of cell P9/10 L in the master cell list (row 273).

@slarson

This comment has been minimized.

Member

slarson commented Jul 30, 2014

Is this one done in the alpha0.5 branch?

@mwatts15

This comment has been minimized.

Contributor

mwatts15 commented Jul 30, 2014

You can query through Cell() for all of the cells listed here:
https://github.com/openworm/PyOpenWorm/blob/alpha0.5/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv

Querying through Neuron does not work.

On Tue, Jul 29, 2014 at 9:51 PM, Stephen Larson notifications@github.com
wrote:

Is this one done in the alpha0.5 branch?


Reply to this email directly or view it on GitHub
#7 (comment).

Cheers,
Mark Watts
Department of Computer Science
University of Texas at Austin

slarson added a commit to openworm/openworm.github.io that referenced this issue Sep 17, 2014

Thanks to a bunch of new contributors!
@jrieke for extensive contributions to
https://github.com/openworm/org.geppetto.recording for GSoC 2014!
@Allysquad for contributions to the windows build instructions of
geppetto: http://docs.geppetto.org/en/latest/windowssetup.html
@balicea for starting up the DevoWorm project and contributions to
PyOpenWorm via this thread:
openworm/PyOpenWorm#7
@dickgordancan for contributions to this thread and DevoWorm:
openworm/PyOpenWorm#7
@StevePMcGrew for contributions to PyOpenWorm:
openworm/PyOpenWorm#8
@travs for contributions to PyOpenWorm:
openworm/PyOpenWorm#48

@slarson slarson removed the in progress label May 21, 2015

@slarson slarson closed this Jun 13, 2015

@slarson

This comment has been minimized.

Member

slarson commented Jun 13, 2015

Pretty sure this got done

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment