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dondi / GRNsight

Web app and service for modeling and visualizing gene regulatory networks.
http://dondi.github.io/GRNsight
BSD 3-Clause "New" or "Revised" License
17 stars 8 forks source link

Prepare lightning talk and poster for BOSC/ISMB 2016 #271

Closed kdahlquist closed 8 years ago

kdahlquist commented 8 years ago

Our abstract: PAPER: 31 TITLE: GRNmap and GRNsight: open source software for dynamical systems modeling and visualization of medium-scale gene regulatory networks AUTHORS: Kam D. Dahlquist, Ben G. Fitzpatrick, John David N. Dionisio, Nicole A. Anguiano, Juan S. Carrillo, Trixie Anne M. Roque, Anindita Varshneya, Mihir Samdarshi and Chukwuemeka E. Azinge

was accepted for a lightning talk at BOSC. I have pasted the reviewer comments below.

OVERALL EVALUATION: 2 (accept -- good for lightning talk, maybe for long talk)

----------- Review ----------- The authors describe two projects, GRNmap and GRNsight, which can be used for modeling and visualisation of gene regulatory networks with a moderate number of genes and edges. Whereas GRNsight was started as an open source project from the beginning, the other project was turned into an open source project after several years of development. This is a good example to show how the involvement of the community can allow a project to grow beyond the means of an individual group. Both tools should be of broad interest.

Specific comments about GRNmap: The readme says that "GRNmap is only compatible with the Windows operating system because of the function it uses to read and write Microsoft Excel spreadsheets". If this is the only restriction then I would highly recommend modifying the tool to work with simpler formats, such as tab-delimited text files and therefore expand the choice of operating systems, particularly since MATLAB compilers are available for Mac OS and Linux. Even though it is handy to have the multiple input files combined as sheets in a single Excel file, I can't see a big problem with providing these as separate tab-delimited text files. The wiki focuses on expression data from yeast strains - does it work with other organisms as well? The input comprises a fairly large set of parameters. Although they are all described in detail it would be good to learn more about the impact any changes would have on the results.

Specific comments about GRNsight: Given that so much emphasis is placed on the testing I would like to mention that one of the tests for GNRsight failed because a file was missing: Error: ENOENT: no such file or directory, open 'test-files/adjacency-matrix-modifications/value-replaced­w-spaces-net-only-input.xlsx' Even though the file seems to be there, the problem arises from a long dash (before the w-spaces) which is represented differently in the Mac file system.

It's very handy to have a public Webserver for GRNsight to avoid the local installation. It works well for quick network visualisations but provides only limited options for modifications (canvas size, node style, node size, node colour, label size, label font, etc.). This makes me think that it might have been better providing some sort of plug-in for Cytoscape instead and use this much more powerful engine instead. But maybe one could offer at least export the network in Cytoscape format or more general in MIMIx format? I could not find an export function for the image either. Are screenshots the only way of generating copies of the networks?

----------------------- REVIEW 2 --------------------- OVERALL EVALUATION: -1 (ok -- good enough for poster)

----------- Review ----------- It is a great idea to port the code to open source, and I value the big effort, even more when there are multiple developers. I don't know how portable this matlab code to octave can be, but I think that it would be good to have the discussion and if possible, have it as a future goal. As well, I look at the documentation, and is quite extensive. I would love to have in the readme what to do to test it with an small example. I noticed a test folder, so I am sure you have plenty of cases. I just miss a few lines in the readme, saying this is how you get it running. It would be something similar to what you have in the GFNsight page, where you have a demo tab there.

----------------------- REVIEW 3 --------------------- OVERALL EVALUATION: 2 (accept -- good for lightning talk, maybe for long talk)

----------- Review ----------- Source was available and the license matched that mentioned in the abstract, BSD license. Thanks!

I would be interested to hear more about the move to GitHub and how that lead to more maintainable software. I have had to make that argument to management/PIs many times over and it is nice to have success stories.

Also, I understand the dependency on MATLAB is sometimes a necessary one; your approach seems reasonable from a user's standpoint, I wonder how tricky it makes reproducibility and validation.

The GRNsight visualizations are quite nice!

kdahlquist commented 8 years ago

Here is the reference for MIMIx format: http://www.nature.com/nbt/journal/v25/n8/full/nbt1324.html

kdahlquist commented 8 years ago

Here is some discussion of Cytoscape vs D3

https://groups.google.com/forum/#!topic/cytoscape-discuss/Ny8_1HuT0vo

http://stackoverflow.com/questions/16776005/what-is-the-difference-between-d3-js-and-cytoscape-js/16992523#16992523

kdahlquist commented 8 years ago

I submitted a slightly revised version of the BOSC abstract last Thursday (6/2), taking into account some of the reviewer feedback.

kdahlquist commented 8 years ago

The BOSC talk is scheduled for 12:21-12:26 on Saturday, July 9. See the BOSC schedule here:

https://www.open-bio.org/wiki/BOSC_2016_Schedule

kdahlquist commented 8 years ago

Poster has been made and uploaded to F1000Research here: http://f1000research.com/posters/5-1618.

kdahlquist commented 8 years ago

Lightning talk slides have now been posted on F1000Research here: http://f1000research.com/slides/5-1637

kdahlquist commented 8 years ago

I decided to post the slides and poster on Slideshare even though they are already on F1000Research.

I've been down the rabbit hole of slideshare for a couple of hours now and the Publications pages of both GRNsight and GRNmap have suffered from it.

Slideshare crashed many times when I was trying to upload slides in the first place because the text I pasted in the description field was too long, but it didn't tell me. I finally figured that out and proceeded to have to search around for the embed code because it was not obvious where that was. I finally figured that out and it turns out that they have changed the code so that the embed code only displays the most recently uploaded presentation, not the specific one that I want. Grrr. I also seemed to mess up something copying and pasting from GRNsight to GRNmap gh-pages code. So, I've deleted some embed code and commented out others and wasted my whole afternoon on this.

I was hoping to simply close this issue and move on, but I need to come back and see what I can do to fix the situation later.

kdahlquist commented 8 years ago

I'm done messing with the GRNsight publications page. Slideshare changed its embed code to create a generic slideshelf and not show a particular presentation. I have simply removed the embed link for the ISMB poster. The next time we upload something to Slideshare, we will have to bear this in mind.

I'm going to spend just a few minutes trying to fix the GRNmap publications page before I close this off for now.

kdahlquist commented 8 years ago

The way to get the embed link for only the presentation you want is to first click the "share" button and it is hidden underneath there.

However, there seems to be a bug that it is not providing a link to the correct presentation, so I'm not going to mess with it further.

There also seems to be a bug on Firefox where the slide won't advance with the slideshelf, but it works on Chrome. I'm just not going to mess with it further. It's just buggy.

I've restored GRNmap publications page to a reasonable state so I'm closing this issue and moving on. Whew!