kdahlquist
commented
4 years ago Dear Kam D. Dahlquist,
Congratulations! An abstract on which you are an author (131, New features for GRNsight: a web application for visualizing models of small- to medium-scale gene regulatory networks) has been chosen for a short talk in the BOSC track of the Bioinformatics Community Conference (BCC2020). Short (lightning) talks are 5 minutes. Long talks are 15 minutes. There will be time allocated at the end of each session for live Q&A with presenters from that session.
All talks at BCC2020 (except for keynotes) will be presented via pre-recorded videos prepared by the presenters (that means you!) and submitted to us by July 6. We will send you more information about this process soon.
In order to accept our invitation to present and secure a spot in our packed schedule, please fill out the response form at https://forms.gle/ZdGeo18tSRpUkffv7 by June 15. If we don’t hear from you by the end of the day on June 15, we will assume you are declining the invitation to give a talk at BCC2020 and will offer your talk spot to another author.
[I accepted the talk and poster/demo options.]
All accepted speakers will also be welcome to present their work as a poster/demo. We're still thinking about how posters and demos will work. We will likely hold them as breakout videoconferences where you can share a live or prerecorded short presentation and a PDF and discuss your work with attendees. We’re also open to suggestions on ways to present posters - a giant poster-sized PDF would not be easy to examine on screens!
If you want to make any changes to the abstract that you submitted, you will have until June 22 to upload a revised abstract at https://easychair.org/conferences/?conf=bcc2020.
Sincerely, Program Committee, BOSC 2020
P.S. The reviewers' feedback on your abstract is at the end of this message. If you have any questions, please contact the BOSC organizing committee bosc@open-bio.org.
SUBMISSION: 131 TITLE: New features for GRNsight: a web application for visualizing models of small- to medium-scale gene regulatory networks
----------------------- REVIEW 1 --------------------- SUBMISSION: 131 TITLE: New features for GRNsight: a web application for visualizing models of small- to medium-scale gene regulatory networks AUTHORS: Kam D. Dahlquist, John David N. Dionisio, Mihir Samdarshi, Nicole A. Anguiano, Anindita Varshneya, Eileen J. Choe, Yeon-Soo Shin, Alexia M. Filler, John L. Lopez, Edward B. Bachoura, Justin Kyle T. Torres, Kevin B. Patterson and Ona O. Igbinedion
----------- Relevant ----------- SCORE: 1 (yes) ----------- Available ----------- SCORE: 1 (yes) ----------- Open ----------- SCORE: 1 (yes) ----------- Updated ----------- SCORE: 1 (project was previously presented at BOSC/GCC but abstract describes updates) ----------- Formatted ----------- SCORE: 1 (yes) ----------- Community ----------- SCORE: 0 (sort of (explain)) ----- TEXT: It mentions where this project can supplement existing solutions in the open source community -- but it's unclear if it will get adoption that way, or an explicit plan for building a community is required. ----------- Novelty ----------- SCORE: 0 (sort of (explain)) ----- TEXT: It very clearly states its extending on an existing project and uses similar tech. However, it has features and use case the original project has. So its showing the evolution of an existing project more so than innovation from my point of view. ----------- Example ----------- SCORE: -1 (no (and it needs one)) ----- TEXT: I feel it needs one -- its talking about a visualization tool and I would've loved to see an example. However, it would mess with the 8.5x11 sized abstract, so I'm not sure where they're supposed to link out to additional images/videos as you recommend. ----------- Runnable ----------- SCORE: 1 (yes) ----- TEXT: It's hosted on a website, which makes it easy to test: https://dondi.github.io/GRNsight/ ----------- Quality score ----------- SCORE: 1 (ok) ----- TEXT: The project itself was well explained, and it was easy to test. However, it was unclear how much impact such a tool has towards science -- what makes it super valuable to what community. ----------- Suitability for a long talk ----------- SCORE: 0 (Ok for poster)
----------------------- REVIEW 2 --------------------- SUBMISSION: 131 TITLE: New features for GRNsight: a web application for visualizing models of small- to medium-scale gene regulatory networks AUTHORS: Kam D. Dahlquist, John David N. Dionisio, Mihir Samdarshi, Nicole A. Anguiano, Anindita Varshneya, Eileen J. Choe, Yeon-Soo Shin, Alexia M. Filler, John L. Lopez, Edward B. Bachoura, Justin Kyle T. Torres, Kevin B. Patterson and Ona O. Igbinedion
----------- Relevant ----------- SCORE: 1 (yes) ----------- Available ----------- SCORE: 1 (yes) ----------- Open ----------- SCORE: 1 (yes) ----------- Updated ----------- SCORE: 1 (project was previously presented at BOSC/GCC but abstract describes updates) ----------- Formatted ----------- SCORE: 1 (yes) ----------- Community ----------- SCORE: 0 (sort of (explain)) ----- TEXT: They mention that some of the new features were prototyped as part of course and capstone project. ----------- Novelty ----------- SCORE: 1 (yes) ----------- Example ----------- SCORE: 0 (sort of or not applicable) ----------- Runnable ----------- SCORE: 0 (sort of or not applicable (explain)) ----- TEXT: I am not a programmer, so I am not sure how to run this software (but that doesn't mean it is not runnable). ----------- Quality score ----------- SCORE: 2 (good) ----- TEXT: This abstract is clearly written and meets all of the criteria. The only thing missing is additional details about how the community can get or is involved. ----------- Suitability for a long talk ----------- SCORE: 1 (Fine for short talk)
----------------------- REVIEW 3 --------------------- SUBMISSION: 131 TITLE: New features for GRNsight: a web application for visualizing models of small- to medium-scale gene regulatory networks AUTHORS: Kam D. Dahlquist, John David N. Dionisio, Mihir Samdarshi, Nicole A. Anguiano, Anindita Varshneya, Eileen J. Choe, Yeon-Soo Shin, Alexia M. Filler, John L. Lopez, Edward B. Bachoura, Justin Kyle T. Torres, Kevin B. Patterson and Ona O. Igbinedion
----------- Relevant ----------- SCORE: 1 (yes) ----------- Available ----------- SCORE: 1 (yes) ----------- Open ----------- SCORE: 1 (yes) ----------- Updated ----------- SCORE: 1 (project was previously presented at BOSC/GCC but abstract describes updates) ----- TEXT: Previously presented at BOSC 2016. The repo shows a large number of commits in the years since it was presented, however, and a large portion of the abstract describes meaningful updates that have been added. ----------- Formatted ----------- SCORE: 1 (yes) ----------- Community ----------- SCORE: 1 (yes) ----- TEXT: This repo has a CoC with clear reporting guidelines, a "people" page for contributors, a good number of contributors on the github repo, wiki, and active issues and pull requests. Oooh, look, a BOSC issue! https://github.com/dondi/GRNsight/issues/869 ----------- Novelty ----------- SCORE: -1 (no) ----- TEXT: Visualising networks is not particularly new in bio sciences, and this tool has been presented before. This is not a problem though - it's better to see a good quality maintained tool (like this one) than a shiny new "novel" approach every year that throws away stable older quality work. ----------- Example ----------- SCORE: 1 (yes) ----- TEXT: There was a nice set of demo graphs I could try out available in the graph vis UI - exactly what I'd hope to see. Nice one! ----------- Runnable ----------- SCORE: 1 (yes) ----- TEXT: instructions are clear and it runs without a single hitch! ----------- Quality score ----------- SCORE: 3 (excellent) ----- TEXT: GRNSight is the sort of abstract that is a delight to review, and should stand as a model for other open source software. It has the well-defined documentation, testing, and continuous integration of a mature software project, with a good project website and an active GitHub repo. This project also takes notice of important but often-ignored aspects such as colourblind friendliness. I especially liked the fact that undergrads develop this with faculty oversight, giving students the chance to learn hands-on open source development skills that will serve them well in the longer term. I would be very happy to see a talk about this at BCC. ----------- Suitability for a long talk ----------- SCORE: 2 (Good for short or long talk)
I submitted an abstract for BOSC 2020 yesterday. It is being held online, so is accessible and the registration fee is very low, $36, so it is affordable, too.
Abstract was committed to master branch documents > abstracts folder: https://github.com/dondi/GRNsight/blob/master/documents/abstracts/Dahlquist_Dionisio_et-al_BOSC_2020_abstract.pdf
Here is the meeting website: https://www.open-bio.org/events/bosc/
Key dates: