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Eviatar
@Eviatar
I can weigh in on this discussion with firsthand knowledge. The annotations in Wormbase are often wrong. In building the NeuroPAL (a strain with landmarks for complete neural ID for the purposes of ID'ing gene expression & neural activity), I've now injected nearly 100 promoters which I would consider to have high-fidelity papers backing the ID (e.g., good markers and/or dye-fill were used, I trust the lab doing the IDs, other precautions were taken, ...). Despite this care, I've found the data to have many mistakes. This sentiment is echoed by many people in our lab including those who completed the IDs for the glutamatergic, cholinergic, & GABAergic neurons (Esther, Laura, & Marie's work; most of these IDs use multiple markers to validate expression -- these are the only IDs I really trust given how much care was taken in validating the expression). The errors in past publication are likely due to the complexity of the task, the variability seen in reporter lines (many genes change their expression at different larval stages, in response to environmental insults such as starvation, and, generally, there are often a lot of weakly expressing cells that are difficult to ID so they're usually ignored). The single-cell transcriptomic work being done now by several labs is likely to fill in the gap with more solid work. For this reason, it might pay to forego the current Wormbase annotations in favor of aggregate consensus from different labs' single-cell transcriptomic work. With regards to specific MNs (e.g., AS1), I'm not sure that we have good markers for many of these (obviously this is necessary if you want to get this kind of cell specificity). I've recently seen a few of FLPs & other genes that target MN subtypes (e.g., VA11/12). Paschalis Kratsios is focused on this specific work and can provide further details and data. Hope that's helpful!
One quick question. Oliver is extremely interested in this type of work. Can I share the spreadsheets with him or are these private? Thanks.
Stephen Larson
@slarson
@Eviatar Thanks for weighing in! The spreadsheets are public; please feel free to share :)
Vahid Ghayoomie
@VahidGh
@Eviatar, Thanks for your informative comments.
It would be really appreciated if you could also get some info from Paschalis regarding cell-specific transcriptions.
David Lung
@lungd
The latest version of the connectome is https://github.com/openworm/PyOpenWorm/blob/master/OpenWormData/aux_data/herm_full_edgelist.csv, right?
In this spreadsheet I can see a gap junction between AVA and AVB (https://github.com/openworm/PyOpenWorm/blob/master/OpenWormData/aux_data/herm_full_edgelist.csv#L6156).
Does this GJ exist in C. elegans? I was told that there should not be a GJ
Eviatar
@Eviatar
AVAR has a GJ with AVBL:
wormwiring.org is an excellent resource for this data
Broadly, C. elegans has 25 innexins. The Altun 2009 paper is a pretty good resource for this data: https://www.ncbi.nlm.nih.gov/pubmed/19621339
The best data for cell-specific transcription is Marie's recent Elife paper:
I think that represents the best data we have to date.
Hope that's helpful!
Eviatar
@Eviatar
Meant Marie for transcription factors. For the transcriptome, there are several public data sets, wormbase.org has a ton of annotations, and Lori's new paper with John White does a great job as well in the supplement: http://www.cell.com/current-biology/fulltext/S0960-9822(16)31212-X
Eviatar
@Eviatar
Forgot about the history & context of this thread. Re-reading it now & realized we were discussing single-cell RNA-Seq. David Miller is visiting Oliver's lab next week. Provided he has time, if you'd like, I can relay a few questions OpenWorm might have regarding the work they're doing with single cell transcriptomics.
Vahid Ghayoomie
@VahidGh
@Eviatar, regarding ion channel genes, the main question is: What is the best gene expression dataset available for adult hermaphrodites to find out ion channel genes being expressed in every specific cell.
For example, egl-19 is a gene encoding an L-Type Calcium channel which has found to be expressed in body wall muscles as well as some neurons, however, I could find only 3 cells that express this gene in the dataset provided by Lori's paper which is not true! (Although, I couldn't find any dataset for the Marie's work!)
Many Microarray datasets available at GEO lack data for many type of ion channel genes in their chipsets, so, I couldn't find useful data at GEO too.
Finally, I need to know if there is any dataset available that includes all ion channel genes in their chipset samples, and the experiment focus on adult C. elegans!
Eviatar
@Eviatar
@VahidGh Marie's paper provides a table with the TFs that pattern differentiation in each neuron (at least what we know to date). You're looking for something else. It should be noted that the data you're after is split in 2. It's easy to ID non-neuronal cells as they tend have distinct morphology & stereotypy in location. On the other hand, neurons require landmarks for ID and so, ion channels present in neurons with good ID is a very sparse data set (this is likely the vast majority of what you're looking for).
You'll notice that for vast families of ion channels (the LGICs for example) so very little is known about their expression.
That is the current state of such work. The data sets that purport to tackle this often present a significant amount of false positives & negatives due to limitations in methodology.
Lori's data set only covers neurons.
Eviatar
@Eviatar
In short, what you're looking for doesn't yet exist. Piecemeal data exists. You can collect it using WormMart: http://wiki.wormbase.org/index.php/Data_mining:WormMart
Hope that helps.
Eviatar
@Eviatar
With regards to Lori's neural data set not being true, what do you think is false? WormBase annotates egl-19 in only 2 neural classes, AWC & the pharyngeal M4.
One thing, since claims of work being untrue in science are usually viewed as strong accusations, I would urge you to use different language in these scenarios.
Eviatar
@Eviatar
Going back to the original comments, I think I see some of the confusion. What I mentioned before is that single-cell transcriptomes are being done now by several labs. What I mean is right now. The data has not yet been published. I know David Miller's lab has been pursuing this. I think Paul Sternberg has been focusing on some of this work as well. When done, this data will have much higher fidelity than what is present in WormBase at the moment ( a collective of published findings, from many different labs, with quite a few errors present due to the difficulty of the work). If you're looking to work with what exists now, you will have to resign yourself to working with what WormBase offers and knowing that this data will change considerably over the next few years.
Vahid Ghayoomie
@VahidGh
@Eviatar, Thanks for your comments. It seems like we should consider other approaches for now. Maybe something like pathway analysis would be more reasonable as suggested by @balicea. If taking this approach, then we should look for the best dataset available for this purpose (or the most comprehensive one)!
Also, it seems the WormMart has been replaced with WormMine since 2016.
And regarding how to use true word :), yes, It would be better to say it's not complete for our purpose.
Steven Cook
@stevenjcook
@lungd @raminmh @slarson , sorry for the delay but I went back to look at the putative AVA / AVB gap junction. It appears as though this is an ambiguous connection that I had scored. When re-analyzing the EMs I wanted to be as sensitive as possible, and this is a connection that I scored despite the quality of the micrographs in this region. You can see what I scored here: http://imgur.com/a/4v9Bg. AVBL is labeled '4' and AVAR is labeled '3'. This connection was only observed once and only between one of the two bilateral pairs, I would not be absolutely certain this connection is representative of all animals.
Ramin Hasani
@raminmh
@stevenjcook thank you for the info. So what would you suggestion about the connectome dataset, shall we continue using it the way it is ( for example about the GJ of the AVA-AVB connection) or not? Thanks
Stephen Larson
@slarson
@stevenjcook -- thanks for this? Any update on the question above?
Sorry..should be thanks for this!
Johnson Chetty
@johnsonc
Hi! Has anyone looked into deducing synaptic weights in biological NNs?
Stephen Larson
@slarson
@johnsonc Hi! Yep; depending on what you mean by “deducing”. What are you thinking of?
Punita Ojha
@punitaojha
This message was deleted
Mayank Mittal
@gmayank32
Hi! Has anyone worked on accessing WPS datasets using python?
Joe Bowen
@joebowen
I just got a message that OpenShift was being sunset and I had a few projects for the openworm project that were running there. Do we need to do anything to move those somewhere? Are they still being used? (pyopenworm-pyopenworm.rhcloud.com, movementvalidation-channelworm.rhcloud.com, channelwormdjango-channelworm.rhcloud.com)
Stephen Larson
@slarson
Hi joe and others! We've moved this over into Slack! Please join us over there.
Joe Bowen
@joebowen
what's your slack url?
Stephen Larson
@slarson
@joebowen openworm.slack.com. Check email!
@gmayank32 haven't heard of WPS. What is it?
Mayank Mittal
@gmayank32
@slarson If you have heard of SAS, it is like other platform to write and compile SAS codes.
a.v.mantzaris
@mantzaris
happy new year. Basic question, what are the different 'types' of neurons in the worm brain?
Eviatar
@Eviatar
a.v.mantzaris
@mantzaris
@Eviatar yes! perfect.
will have to dig up more info on the potential activities
Renato Marinho
@renatomarinho
This message was deleted
Renato Marinho
@renatomarinho
This message was deleted
Afiq
@Cyberknife2221_gitlab
Hye
natakushi
@natakushi
anyone?
Ken Ho
@DrKenHo
Hi