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[PRE REVIEW]: Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape #4961

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@ayush9pandey<!--end-author-handle-- (Ayush Pandey) Repository: https://github.com/biocircuits/bioscrape/ Branch with paper.md (empty if default branch): joss-paper Version: v1.2 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @Farnazmdi, @Robaina Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/5935db21ffab5b33069d05b7adbdf094/status.svg)](https://joss.theoj.org/papers/5935db21ffab5b33069d05b7adbdf094)

Author instructions

Thanks for submitting your paper to JOSS @ayush9pandey. Currently, there isn't a JOSS editor assigned to your paper.

@ayush9pandey 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

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
editorialbot commented 2 years ago

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:

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.43 s (267.3 files/s, 99362.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                             49             76              3           7119
Cython                          11           2126           1985           7019
Python                          24            631           1023           3374
Jupyter Notebook                24              0          15706           2673
TeX                              1             67              0            575
Markdown                         2             55              0            144
MATLAB                           1             19             10             86
YAML                             3              5              4             55
-------------------------------------------------------------------------------
SUM:                           115           2979          18731          21045
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 1506

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1101/121152 is OK

MISSING DOIs

- 10.25080/majora-92bf1922-00a may be a valid DOI for title:  Data Structures for Statistical Computing in Python 
- 10.1109/tcbb.2011.63 may be a valid DOI for title: Parameter estimation using metaheuristics in systems biology: a comprehensive review
- 10.1101/000885 may be a valid DOI for title: Resource usage and gene circuit performance characterization in a cell-free breadboard
- 10.1126/science.1179047 may be a valid DOI for title: Reaction-diffusion model as a framework for understanding biological pattern formation
- 10.1002/chin.200630297 may be a valid DOI for title: Molecular dynamics: survey of methods for simulating the activity of proteins
- 10.1002/anie.201409847 may be a valid DOI for title: Excluded-Volume Effects in Living Cells
- 10.1098/rsfs.2011.0047 may be a valid DOI for title: Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo
- 10.1073/pnas.1200161109 may be a valid DOI for title: Moment-based inference predicts bimodality in transient gene expression
- 10.1038/nmeth.2794 may be a valid DOI for title: Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings
- 10.1038/nature11897 may be a valid DOI for title: Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle
- 10.1186/1471-2105-10-343 may be a valid DOI for title: Bayesian inference of biochemical kinetic parameters using the linear noise approximation
- 10.1007/s11222-007-9043-x may be a valid DOI for title: Bayesian inference for a discretely observed stochastic kinetic model
- 10.1049/iet-syb.2010.0013 may be a valid DOI for title: Identification from stochastic cell-to-cell variation: a genetic switch case study
- 10.1093/bioinformatics/btt380 may be a valid DOI for title: The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations
- 10.1063/1.3664126 may be a valid DOI for title: A data-integrated method for analyzing stochastic biochemical networks
- 10.1038/nature09326 may be a valid DOI for title: Functional roles for noise in genetic circuits
- 10.1007/978-3-642-22110-1_8 may be a valid DOI for title: Parameter identification for Markov models of biochemical reactions
- 10.3182/20140824-6-za-1003.02771 may be a valid DOI for title: Identification of Markov Chains From Distributional Measurements and Applications to Systems Biology
- 10.1109/acc.2016.7524946 may be a valid DOI for title: Linear System Identifiability from Distributional and Time Series Data
- 10.1038/nrmicro2056 may be a valid DOI for title: Using movies to analyse gene circuit dynamics in single cells
- 10.1006/jmbi.1993.1092 may be a valid DOI for title: Quantitative Model of ColE1 Plasmid Copy Number Control
- 10.1036/1097-8542.yb130009 may be a valid DOI for title: RNA Mimics of Green Fluorescent Protein
- 10.23943/princeton/9780691161532.001.0001 may be a valid DOI for title: Biomolecular Feedback Systems
- 10.1109/mcse.2010.118 may be a valid DOI for title: Cython: The Best of Both Worlds
- 10.1371/journal.pone.0079345 may be a valid DOI for title: StochPy: A Comprehensive, User-Friendly Tool for Simulating Stochastic Biological Processes
- 10.1073/pnas.1013171108 may be a valid DOI for title: Random partitioning of molecules at cell division
- 10.1038/nprot.2011.432 may be a valid DOI for title: Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy
- 10.1109/tbcas.2016.2526668 may be a valid DOI for title: Mechanistic Modeling of a Rewritable Recombinase Addressable Data Module
- 10.1126/science.aad8559 may be a valid DOI for title: Synthetic recombinase-based state machines in living cells
- 10.1073/pnas.1202344109 may be a valid DOI for title: Rewritable digital data storage in live cells via engineered control of recombination directionality.
- 10.1101/2020.08.02.233478 may be a valid DOI for title: BioCRNpyler: compiling chemical reaction networks from biomolecular parts in diverse contexts
- 10.1101/029967 may be a valid DOI for title: A population-based temporal logic gate for timing and recording chemical events.
- 10.1046/j.1365-2958.2002.02891.x may be a valid DOI for title: Diversity in the serine recombinases
- 10.1016/j.jmb.2003.09.082 may be a valid DOI for title: Phage Integrases: Biology and Applications 
- 10.2140/camcos.2010.5.65 may be a valid DOI for title: Ensemble Samplers with Affine Invariance
- 10.1016/j.cell.2008.01.027 may be a valid DOI for title: Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination
- 10.1186/1754-1611-2-5 may be a valid DOI for title: Engineering BioBrick vectors from BioBrick parts
- 10.1038/nbt.2401 may be a valid DOI for title: Ribozyme-based insulator parts buffer synthetic circuits from genetic context

INVALID DOIs

- None
ayush9pandey commented 2 years ago

Fixed the missing doi's. Adding co-first author @WilliamIX to this review.

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/tcbb.2011.63 is OK
- 10.1101/000885 is OK
- 10.1126/science.1179047 is OK
- 10.1002/chin.200630297 is OK
- 10.1002/anie.201409847 is OK
- 10.1098/rsfs.2011.0047 is OK
- 10.1073/pnas.1200161109 is OK
- 10.1038/nmeth.2794 is OK
- 10.1038/nature11897 is OK
- 10.1186/1471-2105-10-343 is OK
- 10.1007/s11222-007-9043-x is OK
- 10.1049/iet-syb.2010.0013 is OK
- 10.1093/bioinformatics/btt380 is OK
- 10.1063/1.3664126 is OK
- 10.1038/nature09326 is OK
- 10.1007/978-3-642-22110-1_8 is OK
- 10.3182/20140824-6-za-1003.02771 is OK
- 10.1109/acc.2016.7524946 is OK
- 10.1038/nrmicro2056 is OK
- 10.1006/jmbi.1993.1092 is OK
- 10.1036/1097-8542.yb130009 is OK
- 10.23943/princeton/9780691161532.001.0001 is OK
- 10.1109/mcse.2010.118 is OK
- 10.1371/journal.pone.0079345 is OK
- 10.1073/pnas.1013171108 is OK
- 10.1038/nprot.2011.432 is OK
- 10.1109/tbcas.2016.2526668 is OK
- 10.1126/science.aad8559 is OK
- 10.1073/pnas.1202344109 is OK
- 10.1371/journal.pcbi.1009987 is OK
- 10.1002/rnc.6013 is OK
- 10.1101/029967 is OK
- 10.1046/j.1365-2958.2002.02891.x is OK
- 10.1016/j.jmb.2003.09.082 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1016/j.cell.2008.01.027 is OK
- 10.1186/1754-1611-2-5 is OK
- 10.1038/nbt.2401 is OK

MISSING DOIs

- 10.1101/2022.10.05.511053 may be a valid DOI for title: Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline

INVALID DOIs

- None
ayush9pandey commented 2 years ago

Fixed the last missing doi!

@editorialbot check references

ayush9pandey commented 2 years ago

Here's our suggested list of reviewers from the JOSS provided list:

  1. arghdos,
  2. Farnazmdi,
  3. espottesmith
ayush9pandey commented 1 year ago

@Kevin-Mattheus-Moerman sorry for the ping, but was just wondering if you could run the check references command.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot check references

@ayush9pandey sure although you are also permitted to call that command

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/tcbb.2011.63 is OK
- 10.1101/000885 is OK
- 10.1126/science.1179047 is OK
- 10.1002/chin.200630297 is OK
- 10.1002/anie.201409847 is OK
- 10.1098/rsfs.2011.0047 is OK
- 10.1073/pnas.1200161109 is OK
- 10.1038/nmeth.2794 is OK
- 10.1038/nature11897 is OK
- 10.1186/1471-2105-10-343 is OK
- 10.1007/s11222-007-9043-x is OK
- 10.1049/iet-syb.2010.0013 is OK
- 10.1093/bioinformatics/btt380 is OK
- 10.1063/1.3664126 is OK
- 10.1038/nature09326 is OK
- 10.1007/978-3-642-22110-1_8 is OK
- 10.3182/20140824-6-za-1003.02771 is OK
- 10.1109/acc.2016.7524946 is OK
- 10.1038/nrmicro2056 is OK
- 10.1006/jmbi.1993.1092 is OK
- 10.1036/1097-8542.yb130009 is OK
- 10.23943/princeton/9780691161532.001.0001 is OK
- 10.1109/mcse.2010.118 is OK
- 10.1371/journal.pone.0079345 is OK
- 10.1073/pnas.1013171108 is OK
- 10.1038/nprot.2011.432 is OK
- 10.1109/tbcas.2016.2526668 is OK
- 10.1126/science.aad8559 is OK
- 10.1073/pnas.1202344109 is OK
- 10.1371/journal.pcbi.1009987 is OK
- 10.1002/rnc.6013 is OK
- 10.1101/029967 is OK
- 10.1046/j.1365-2958.2002.02891.x is OK
- 10.1016/j.jmb.2003.09.082 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1016/j.cell.2008.01.027 is OK
- 10.1186/1754-1611-2-5 is OK
- 10.1101/2022.10.05.511053 is OK
- 10.1038/nbt.2401 is OK

MISSING DOIs

- None

INVALID DOIs

- None
ayush9pandey commented 1 year ago

Fixed the last missing doi!

@editorialbot check references

I tried above, but it didn't work. Maybe it was because I didn't start the message with that command. Thanks for your help!

Do you know how long it would usually take for an editor to start the review process for this paper?

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot invite @lucydot as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot invite @csoneson as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

csoneson commented 1 year ago

@editorialbot assign @csoneson as editor

editorialbot commented 1 year ago

Assigned! @csoneson is now the editor

csoneson commented 1 year ago

👋🏻 @ayush9pandey - I will handle your submission and start by inviting reviewers (thanks for the suggestions above)!

csoneson commented 1 year ago

👋🏻 @arghdos, @Farnazmdi, @espottesmith - would two of you be interested in reviewing this submission for JOSS?

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape

csoneson commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

csoneson commented 1 year ago

I tried above, but it didn't work. Maybe it was because I didn't start the message with that command.

@ayush9pandey - yes, the editorialbot commands need to be given first in the message.

Farnazmdi commented 1 year ago

I would be happy to review this!

csoneson commented 1 year ago

Brilliant, thanks @Farnazmdi - as soon as we have one more reviewer I will assign you and start the review issue.

csoneson commented 1 year ago

👋🏻 @smsaladi, @ayaanhossain - would you be interested in reviewing this submission for JOSS?

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape

ayush9pandey commented 1 year ago

Would be great if one of the reviewers already tagged here would respond. But in case they are not interested/don't have the bandwidth, we may request one of jguhlin, Robaina, or Maocx to review.

csoneson commented 1 year ago

@jguhlin, @Robaina - would one of you be interested in reviewing this submission for JOSS?

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape

Robaina commented 1 year ago

Hi @csoneson, @ayush9pandey,

I could review this submission if you are interested.

csoneson commented 1 year ago

@Robaina that's great, thanks a lot!

As we now have two reviewers secured, I will assign you and start the review issue.

csoneson commented 1 year ago

@editorialbot add @Farnazmdi as reviewer

editorialbot commented 1 year ago

@Farnazmdi added to the reviewers list!

csoneson commented 1 year ago

@editorialbot add @Robaina as reviewer

editorialbot commented 1 year ago

@Robaina added to the reviewers list!

csoneson commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5057.