[PRE REVIEW]: NORDic: a Network-Oriented package for the Repurposing of Drugs

[editorialbot]

Submitting author: !--author-handle-->@clreda<!--end-author-handle-- (Clémence Réda) Repository: https://github.com/clreda/NORDic Branch with paper.md (empty if default branch): Version: v2.4.2 Editor: !--editor-->@lpantano<!--end-editor-- Reviewers: @cauliyang, @sevgisu0227 Managing EiC: Kevin M. Moerman

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Author instructions

Thanks for submitting your paper to JOSS @clreda. Currently, there isn't a JOSS editor assigned to your paper.

@clreda if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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[editorialbot]

Hello human, 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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.56 s (85.8 files/s, 100525.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Python                          26            421           1321           4276
Jupyter Notebook                10              0          48360            907
TeX                              1             39              0            371
Markdown                         2             62              0            181
YAML                             4             15              0            159
JSON                             3              0              0             72
ASP                              1              1              0             58
TOML                             1              0              0              3
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SUM:                            48            538          49681           6027
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2118

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1016/0022-5193(74)90172-6 may be a valid DOI for title: Boolean formalization of genetic control circuits
- 10.1016/0022-5193(69)90015-0 may be a valid DOI for title: Metabolic stability and epigenesis in randomly constructed genetic nets
- 10.1093/bioinformatics/btx123 may be a valid DOI for title: MaBoSS 2.0: an environment for stochastic Boolean modeling
- 10.1038/npjsba.2016.15 may be a valid DOI for title: L1000CDS2: LINCS L1000 characteristic direction signatures search engine
- 10.1093/cid/ciab350 may be a valid DOI for title: Supporting drug development for neglected tropical diseases using mathematical modeling
- 10.1016/j.cell.2008.09.050 may be a valid DOI for title: Nature, nurture, or chance: stochastic gene expression and its consequences
- 10.1073/pnas.1533293100 may be a valid DOI for title: Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics
- 10.1007/978-3-031-15034-0_5 may be a valid DOI for title: Prioritization of Candidate Genes Through Boolean Networks
- 10.1109/ictai.2019.00014 may be a valid DOI for title: Synthesis of Boolean networks from biological dynamical constraints using answer-set programming
- 10.1038/npjsba.2016.10 may be a valid DOI for title: A method to identify and analyze biological programs through automated reasoning
- 10.1101/2020.05.27.119016 may be a valid DOI for title: Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers
- 10.1093/bioinformatics/btq124 may be a valid DOI for title: BoolNet—an R package for generation, reconstruction and analysis of Boolean networks
- 10.1038/npjsba.2016.20 may be a valid DOI for title: MINERVA—a platform for visualization and curation of molecular interaction networks
- 10.1093/bioinformatics/btaa484 may be a valid DOI for title: Automated inference of Boolean models from molecular interaction maps using CaSQ
- 10.1371/journal.pone.0044459 may be a valid DOI for title: Control centrality and hierarchical structure in complex networks
- 10.1101/gr.1239303 may be a valid DOI for title: Cytoscape: a software environment for integrated models of biomolecular interaction networks
- 10.1093/bioinformatics/btx764 may be a valid DOI for title: CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis
- 10.1038/s41598-019-54180-4 may be a valid DOI for title: A framework for identification of on-and off-target transcriptional responses to drug treatment
- 10.1145/956750.956769 may be a valid DOI for title: Maximizing the spread of influence through a social network
- 10.1038/nmeth.4077 may be a valid DOI for title: OmniPath: guidelines and gateway for literature-curated signaling pathway resources
- 10.1093/nar/gkw943 may be a valid DOI for title: DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
- 10.1093/bib/bbw112 may be a valid DOI for title: A review of connectivity map and computational approaches in pharmacogenomics

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@clreda thanks for this submission. I am the AEiC for this track and here to help with the initial steps. I have started looking for a handling editor, however all are currently busy handling other submissions. I'll have to waitlist this submission until an editor in this domain becomes available. In the meantime please can you try to address those potentially missing DOIs :point_up: ? You can update the bib file and then call @editorialbot check references, you can also call @editorialbot generate pdf to update the paper. (Note one should also remove any references from the bib file that are not cited in the paper, so work on that too if needed). Thanks.

[clreda]

Potential reviewers:

ammaraziz NoujoudNader kalilamali Cagret Djgies jguhlin Robaina canimus cauliyang kdhusia

[clreda]

@clreda thanks for this submission. I am the AEiC for this track and here to help with the initial steps. I have started looking for a handling editor, however all are currently busy handling other submissions. I'll have to waitlist this submission until an editor in this domain becomes available. In the meantime please can you try to address those potentially missing DOIs point_up ? You can update the bib file and then call @editorialbot check references, you can also call @editorialbot generate pdf to update the paper. (Note one should also remove any references from the bib file that are not cited in the paper, so work on that too if needed). Thanks.

Thank you for your work @Kevin-Mattheus-Moerman. I will tackle the reference issue in the meantime.

[clreda]

@editorialbot check references

[clreda]

@editorialbot generate pdf

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1172/JCI66220 is OK
- 10.1038/nrm2503 is OK
- 10.1016/0022-5193(74)90172-6 is OK
- 10.1016/0022-5193(69)90015-0 is OK
- 10.48550/arXiv.2212.12756 is OK
- 10.1038/s41598-020-73147-4 is OK
- 10.1038/s41467-018-06008-4 is OK
- 10.1038/npjsba.2016.15 is OK
- 10.1093/cid/ciab350 is OK
- 10.1073/pnas.1610622114 is OK
- 10.1016/j.cell.2008.09.050 is OK
- 10.1073/pnas.1533293100 is OK
- 10.48550/arXiv.2111.01479 is OK
- 10.1007/978-3-031-15034-0_5 is OK
- 10.1186/s13059-016-1097-7 is OK
- 10.1186/1471-2105-7-S1-S7 is OK
- 10.1093/bioinformatics/btr274 is OK
- 10.1109/ictai.2019.00014 is OK
- 10.1038/npjsba.2016.10 is OK
- 10.1371/journal.pcbi.1007900 is OK
- 10.1093/bioinformatics/btq124 is OK
- 10.1038/npjsba.2016.20 is OK
- 10.1093/bioinformatics/btaa484 is OK
- 10.48550/arXiv.2103.10070 is OK
- 10.1371/journal.pone.0044459 is OK
- 10.1101/gr.1239303 is OK
- 10.1093/bioinformatics/btx764 is OK
- 10.1093/bioinformatics/btv305 is OK
- 10.1038/s41598-019-54180-4 is OK
- 10.1145/956750.956769 is OK
- 10.1101/2020.05.27.119016 is OK
- 10.1016/j.cell.2017.10.049 is OK
- 10.1038/nmeth.4077 is OK
- 10.1093/nar/gkw943 is OK
- 10.1093/nar/gkaa1074 is OK
- 10.1093/bib/bbw112 is OK
- 10.5281/zenodo.7239047 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@britta-wstnr do you think you could help edit this submission? It may be somewhat off topic.

[britta-wstnr]

@Kevin-Mattheus-Moerman this is indeed quite far from my own expertise. As a newer editor, I could use some guidance in seeing if this is still within my focus - I wrote you a PM about it.

[Kevin-Mattheus-Moerman]

@editorialbot @lpantano as editor

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[Kevin-Mattheus-Moerman]

@editorialbot invite @lpantano as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@lpantano do you think you can help edit this one? Thanks!

[lpantano]

Hi Kevin, I don't think I have time right now. Probably in one or two week. Sorry for the delay responding.

[Kevin-Mattheus-Moerman]

Hi @lpantano thanks for getting back to me. Do you mind if I assign you now but that we leave it waitlisted for the moment, and resume/start whenever you are ready?

[lpantano]

sounds good!

[Kevin-Mattheus-Moerman]

@editorialbot assign @lpantano as editor

[editorialbot]

Assigned! @lpantano is now the editor

[lpantano]

Hi, starting with this now. @clreda, any suggestions for reviewers? thanks

[clreda]

Thanks a lot @lpantano for accepting to edit this submission. This is the list of potential reviewers:

ammaraziz NoujoudNader kalilamali Cagret Djgies jguhlin Robaina canimus cauliyang kdhusia

[lpantano]

Hi @cauliyang, would you like to review this tool?

[cauliyang]

Hi @lpantano, Thanks for the invitation, and I am happy to review the tool. But I wonder, is there something I need to pay attention to? What is the timeline?

[lpantano]

@editorialbot add @cauliyang as reviewer

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[lpantano]

@editorialbot add @cauliyang to reviewers

[editorialbot]

@cauliyang added to the reviewers list!

[lpantano]

@editorialbot add @sevgisu0227 to reviewers

[editorialbot]

@sevgisu0227 added to the reviewers list!

[lpantano]

Thanks @cauliyang, and @sevgisu0227 to accept to review this tool. I will close this issue and it will open with the checklist of things to look during reviewing. Similar to this: https://joss.readthedocs.io/en/latest/review_checklist.html. Timeline usually is inside 2 weeks, but it highly depends on how many things need to be addressed by authors as you go through the checklist. Thanks!

[lpantano]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5532.