Closed editorialbot closed 1 year ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.08 s (816.0 files/s, 141155.7 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
SQL 2 2 0 4085
Python 32 784 1177 2721
reStructuredText 12 286 84 496
TeX 1 29 0 378
JSON 5 0 0 268
YAML 8 31 45 206
INI 1 14 0 174
Markdown 2 57 0 174
C Shell 1 20 10 30
-------------------------------------------------------------------------------
SUM: 64 1223 1316 8532
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1626
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1146/annurev.biophys.37.092707.153558 is OK
- 10.1080/152165401317291147 is OK
- 10.1136/mp.53.1.8 is OK
- 10.1016/j.sbi.2019.05.024 is OK
- 10.1016/j.sbi.2007.01.009 is OK
- 10.1093/bioinformatics/bts172 is OK
- 10.1002/(sici)1097-0134(20000501)39:2<112::aid-prot2>3.0.co;2-b is OK
- 10.1002/prot.1163 is OK
- 10.1021/acs.jpcb.0c02924 is OK
- 10.1021/acs.jpca.2c03726 is OK
- 10.1016/j.str.2018.10.016 is OK
- 10.1093/nar/28.1.235 is OK
- 10.1093/bioinformatics/bts701 is OK
- 10.1021/jacs.6b00351 is OK
- 10.1038/s42004-020-0323-0 is OK
- 10.1007/978-1-0716-0270-6_15 is OK
- 10.1039/c9sc06561j is OK
- 10.1107/s1600576717007786 is OK
- 10.1016/j.bpj.2018.01.002 is OK
- 10.1021/ja0000908 is OK
MISSING DOIs
- 10.1021/acs.jpclett.6b00885.s001 may be a valid DOI for title: Multi-timescale dynamics in intrinsically disordered proteins from NMR relaxation and molecular simulation
- 10.1101/2020.08.09.243030 may be a valid DOI for title: DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
- 10.1021/jacs.1c06264.s001 may be a valid DOI for title: Quantitative description of intrinsically disordered proteins using single-molecule FRET, NMR, and SAXS
INVALID DOIs
- None
Hello @menoliu, here are the things you can ask me to do:
# List all available commands
@editorialbot commands
# Get a list of all editors's GitHub handles
@editorialbot list editors
# Check the references of the paper for missing DOIs
@editorialbot check references
# Perform checks on the repository
@editorialbot check repository
# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist
# Set a value for branch
@editorialbot set joss-paper as branch
# Generates the pdf paper
@editorialbot generate pdf
# Generates a LaTeX preprint file
@editorialbot generate preprint
# Get a link to the complete list of reviewers
@editorialbot list reviewers
Just a minor note to the editor and reviewers that since v0.1.10, I've fixed some minor bugs and the most up-to-date version is v0.1.13. Thanks!
@editorialbot add @lohedges as reviewer
@lohedges added to the reviewers list!
Thank you @lohedges for agreeing to review this. If you have any questions at any point please let me know. You can generate your review checklist with the following command: @editorialbot generate my checklist
.
Sorry folks for the delay, working against a deadline. Have this on my task list for later this week.
no worries @dotsdl thanks for getting started with this!
@dotsdl and @lohedges, I've just sent you a gentle reminder email for this review.
Apologies Lester for the delayed response to the issues, I was not notified via E-mail... They will all be resolved in the first week* of January. Happy holidays!
Edit: by the end of the month*, I've rang in the new year with COVID-19.
@menoliu: Thanks for your updates. I've not had a chance to look at these yet and won't for the next week or so since I'm working to some tight deadlines.
Thanks @lohedges and @menoliu for the updates. @dotsdl How are you getting on with your review?
Thank you all for your notes and reviews. I am making improvements to SPyCi-PDB currently as well as one of my projects demand it. I will be modifying the chemical-shift (CS) back-calculator by adding another, more commonly used one, perhaps as the default to hopefully resolve some current/initial issues (I will be more than happy to edit the manuscript if needed later on). Cheers!
@dotsdl had to, unfortunately, drop out as a reviewer. @menoliu I am trying to secure a second reviewer. If you have any suggestions they'd be very welcome.
@lohedges did you manage to be able to take a look at the updates?
Not yet, I'm afraid. I doubt I'll be able to do so until the middle/end of next week at the earliest, I'm afraid.
Sorry for the late reply @ppxasjsm I was at a conference. I believe if nicksisco1932 or sulstice are available that would be great.
Hi @ppxasjsm , hope you're doing well. Just wondering how is it securing another reviewer? Thanks in advance!
Hi @menoliu, now I had accidentally dropped the ball. Too many deadlines and then I got sick. On it now.
@editorialbot add @JenkeScheen to reviewers
@JenkeScheen added to the reviewers list!
@JenkeScheen thank you for agreeing to review this submission! You can generate your checklist using the command @editorialbot generate my checklist
.
Sure
On Fri, Mar 24, 2023 at 10:46 AM Toni Mey @.***> wrote:
@JenkeScheen https://github.com/JenkeScheen thank you for agreeing to review this submission! You can generate your checklist using the command @editorialbot generate my checklist.
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4861#issuecomment-1482923006, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2EAUUT3ZXWBPOPQ5C7RTTW5WXSTANCNFSM6AAAAAARHKVMVE . You are receiving this because you were mentioned.Message ID: @.***>
-- Suliman Sharif Ph.D. Candidate Pharmaceutical Sciences | University of Maryland, School of Pharmacy M.Sc Medicinal Chemistry | University of California, Riverside School of Medicine B.Sc. Biochemistry | University of Texas at Austin @.***
@editorialbot add @sulstice to reviewers
@sulstice added to the reviewers list!
Thank you @Sulstice!
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@Sulstice are you able to do the review?
@JenkeScheen Thanks for your review on #43. I have since updated the manuscript as well as included plotting functions for the modules shown as figures in the paper (rh
, jc
, noe
, pre
). I have also noticed your checkbox on Installation instructions:
and have updated the documentation to include a clear list of dependencies as well.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thanks @menoliu! The additional figures look great. I'll let @lohedges give his thoughts on the updated installation instructions.
Many thanks @menoliu, I can confirm that the fixes work as expected and the installation process is now a lot more streamlined. Longer term, I still think it would be beneficial to make pip
or conda
packages for both SPyCi-PDB
and IDPConformerGenerator
, as it would make it easier to install your tools into larger environments alongside other packages.
I've left the references section unchecked at present since there is a minor formatting issue. I'll open an issue for that.
@JenkeScheen: Thanks for the comments regarding the additional examples and figures. The updates are really helpful.
Cheers.
Thank you so much @lohedges for the comments. I have addressed them in the latest PR #47. The documentation is much cleaner now I think.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@ppxasjsm thanks for organizing reviewers and keeping everyone up to date throughout this review process. I was just wondering since both Lester and Jenke have completed the checklist, what are the next steps moving forward?
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1146/annurev.biophys.37.092707.153558 is OK
- 10.1080/152165401317291147 is OK
- 10.1136/mp.53.1.8 is OK
- 10.1016/j.sbi.2019.05.024 is OK
- 10.1016/j.sbi.2007.01.009 is OK
- 10.1093/bioinformatics/bts172 is OK
- 10.1002/(sici)1097-0134(20000501)39:2<112::aid-prot2>3.0.co;2-b is OK
- 10.1002/prot.1163 is OK
- 10.1021/acs.jpcb.0c02924 is OK
- 10.1021/acs.jpca.2c03726 is OK
- 10.1016/j.str.2018.10.016 is OK
- 10.1093/nar/28.1.235 is OK
- 10.1093/bioinformatics/bts701 is OK
- 10.1021/jacs.6b00351 is OK
- 10.1038/s42004-020-0323-0 is OK
- 10.1007/978-1-0716-0270-6_15 is OK
- 10.1039/c9sc06561j is OK
- 10.1107/s1600576717007786 is OK
- 10.1016/j.bpj.2018.01.002 is OK
- 10.1021/ja0000908 is OK
MISSING DOIs
- 10.1021/acs.jpclett.6b00885.s001 may be a valid DOI for title: Multi-timescale dynamics in intrinsically disordered proteins from NMR relaxation and molecular simulation
- 10.1021/jacs.1c06264.s001 may be a valid DOI for title: Quantitative description of intrinsically disordered proteins using single-molecule FRET, NMR, and SAXS
INVALID DOIs
- None
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1146/annurev.biophys.37.092707.153558 is OK
- 10.1080/152165401317291147 is OK
- 10.1136/mp.53.1.8 is OK
- 10.1016/j.sbi.2019.05.024 is OK
- 10.1038/s41586-021-03819-2 is OK
- 10.1126/science.abj8754 is OK
- 10.1016/j.sbi.2007.01.009 is OK
- 10.1093/bioinformatics/bts172 is OK
- 10.1002/(sici)1097-0134(20000501)39:2<112::aid-prot2>3.0.co;2-b is OK
- 10.1002/prot.1163 is OK
- 10.1021/acs.jpcb.0c02924 is OK
- 10.1021/acs.jpca.2c03726 is OK
- 10.1016/j.str.2018.10.016 is OK
- 10.1093/nar/28.1.235 is OK
- 10.1021/acs.jpclett.6b00885 is OK
- 10.1073/pnas.1800690115 is OK
- 10.1093/bioinformatics/bts701 is OK
- 10.1021/jacs.6b00351 is OK
- 10.48550/ARXIV.2206.12667 is OK
- 10.1038/s42004-020-0323-0 is OK
- 10.1007/978-1-0716-0270-6_15 is OK
- 10.1039/c9sc06561j is OK
- 10.1021/ja003724j is OK
- 10.1107/s1600576717007786 is OK
- 10.1016/j.bpj.2018.01.002 is OK
- 10.1021/ja0000908 is OK
- 10.1021/jacs.1c06264 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
I’ll now go through the submission make sure everything’s is in order. I may raise a couple more issues and then we can proceed with the publication. I probably will only get a chance to look at this properly next week though I am afraid. I’ll post anything I’ll need from you here or as an issue!
Sorry just to let you know that I didn't find time due to a looming deadline on Monday. I'll get to look at this for sure early next week. My apologies for the delay.
Thanks for the heads up! Looking forwards to the next steps.
@menoliu, I've created a small issue for editorial suggestions of the paper: https://github.com/julie-forman-kay-lab/SPyCi-PDB/issues/51
Please read your publication again and create a new release of the software that reflects the paper version of it. Then deposit this version of the software on Zenodo or Figshare and post the DOI for it here.
Submitting author: !--author-handle-->@menoliu<!--end-author-handle-- (Zi Hao Liu) Repository: https://github.com/julie-forman-kay-lab/SPyCi-PDB Branch with paper.md (empty if default branch): Version: v0.3.5 Editor: !--editor-->@ppxasjsm<!--end-editor-- Reviewers: @dotsdl, @lohedges, @JenkeScheen, @sulstice Archive: 10.5281/zenodo.7887039
Status
Status badge code:
Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@dotsdl, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @ppxasjsm know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
Checklists
📝 Checklist for @dotsdl
📝 Checklist for @lohedges
📝 Checklist for @JenkeScheen