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[PRE REVIEW]: pyABC: Efficient and robust easy-to-use approximate Bayesian computation #4285

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@yannikschaelte<!--end-author-handle-- (Yannik Schälte) Repository: https://github.com/icb-dcm/pyabc Branch with paper.md (empty if default branch): joss_0_12 Version: 0.12.2 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @mattpitkin, @hpesonen Managing EiC: Kyle Niemeyer

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Markdown: [![status](https://joss.theoj.org/papers/2d6356cc20804387a631e481d5124d6e/status.svg)](https://joss.theoj.org/papers/2d6356cc20804387a631e481d5124d6e)

Author instructions

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

The author's suggestion for the handling editor is @jedbrown.

@yannikschaelte 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).

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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:

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editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.63 s (437.8 files/s, 83348.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         174           5425           8799          18305
Jupyter Notebook                23              0          10743           2310
SVG                             11              6              6           1831
reStructuredText                35            877            345           1496
TeX                              1             50              0            584
YAML                             6             75             16            339
HTML                             7             33              0            288
INI                              2             38              0            221
make                             1             29              6            181
XML                              1              1              1            152
Markdown                         4             31              0            124
Bourne Shell                     2             19             22             99
R                                6             28             46             84
Julia                            2             16             13             50
Mako                             1              7              0             17
TOML                             1              3              3             14
-------------------------------------------------------------------------------
SUM:                           277           6638          20000          26095
-------------------------------------------------------------------------------

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

Wordcount for paper.md is 1329

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

OK DOIs

- 10.1145/3093172.3093233 is OK
- 10.1111/2041-210X.12050 is OK
- 10.1101/2022.03.18.484896 is OK
- 10.1515/sagmb-2013-0010 is OK
- 10.1093/bioinformatics/btaa397 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1371/journal.pcbi.1008646 is OK
- 10.1093/bioinformatics/btab227 is OK

MISSING DOIs

- 10.1093/genetics/145.2.505 may be a valid DOI for title: Inferring coalescence times from DNA sequence data
- 10.1038/nrg2509 may be a valid DOI for title: Stochastic modelling for quantitative description of heterogeneous biological systems
- 10.1016/j.cels.2016.12.002 may be a valid DOI for title: Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models
- 10.1214/07-aos574 may be a valid DOI for title: The pseudo-marginal approach for efficient Monte Carlo computations
- 10.1093/oxfordjournals.molbev.a026091 may be a valid DOI for title: Population growth of human Y chromosomes: a study of Y chromosome microsatellites.
- 10.1093/genetics/162.4.2025 may be a valid DOI for title: Approximate Bayesian Computation in Population Genetics
- 10.1093/bioinformatics/btaa078 may be a valid DOI for title: GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation
- 10.1093/bioinformatics/bty361 may be a valid DOI for title: pyABC: distributed, likelihood-free inference
- 10.1515/sagmb-2012-0069 may be a valid DOI for title: On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo
- 10.1007/978-3-319-67471-1_8 may be a valid DOI for title: A scheme for adaptive selection of population sizes in Approximate Bayesian Computation - Sequential Monte Carlo
- 10.1038/s41467-019-09879-3 may be a valid DOI for title: Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures
- 10.1101/2020.05.10.20097469 may be a valid DOI for title: Covasim: an agent-based model of COVID-19 dynamics and interventions
- 10.1063/5.0010764 may be a valid DOI for title: A multiscale compartment-based model of stochastic gene regulatory networks using hitting-time analysis
- 10.1101/2022.02.10.479738 may be a valid DOI for title: Inferring cell motility in complex environments with incomplete tracking data
- 10.1088/1475-7516/2021/08/027 may be a valid DOI for title: Towards a model-independent reconstruction approach for late-time Hubble data
- 10.1016/j.compbiomed.2018.10.015 may be a valid DOI for title: Rethinking multiscale cardiac electrophysiology with machine learning and predictive modelling
- 10.1002/eap.2442 may be a valid DOI for title: Inferring pesticide toxicity to honey bees from a field-based feeding study using a colony model and Bayesian inference
- 10.1101/2021.07.29.454327 may be a valid DOI for title: Robust adaptive distance functions for approximate Bayesian inference on outlier-corrupted data
- 10.1214/16-ba1002 may be a valid DOI for title: Adapting the ABC Distance Function
- 10.1214/12-sts406 may be a valid DOI for title: A comparative review of dimension reduction methods in approximate Bayesian computation
- 10.1111/j.1467-9868.2011.01010.x may be a valid DOI for title: Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation
- 10.5705/ss.202015.0340 may be a valid DOI for title: Learning summary statistic for approximate Bayesian computation via deep neural network
- 10.1016/j.jcp.2020.109999 may be a valid DOI for title: Gaussian process enhanced semi-automatic approximate Bayesian computation: parameter inference in a stochastic differential equation system for chemotaxis
- 10.1515/sagmb-2012-0043 may be a valid DOI for title: Optimizing threshold-schedules for sequential approximate Bayesian computation: Applications to molecular systems
- 10.1111/j.1541-0420.2010.01410.x may be a valid DOI for title: Estimation of parameters for macroparasite population evolution using approximate Bayesian computation
- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1093/bioinformatics/btp619 may be a valid DOI for title: Simulation-based model selection for dynamical systems in systems and population biology

INVALID DOIs

- None
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:

kyleniemeyer commented 2 years ago

@editorialbot invite @osorensen as editor

Hi @osorensen, could you edit this?

editorialbot commented 2 years ago

Invitation to edit this submission sent!

kyleniemeyer commented 2 years ago

Hi @yannikschaelte, we will use this issue to get the editor and then reviewers assigned. In the meantime, could you take a look at the missing DOIs in your paper pointed out above? Thanks!

osorensen commented 2 years ago

@editorialbot assign @osorensen as editor

editorialbot commented 2 years ago

Assigned! @osorensen is now the editor

yannikschaelte commented 2 years ago

Hi @kyleniemeyer @osorensen ! Sure, I will address the missing DOIs. Should I then simply update the paper.bib file, or should additional actions be performed?

Regarding reviewers, I think especially persons working on statistical inference, parameter inference and(/or) systems/computational biology (nhejazi, krother, khinsen, cthoyt, dirmeier, blakeaw, GregoryAshton, mattpitkin, marouenbg, dsurujon) or specifically approximate Bayesian computation / likelihood-free inference (janfb, matt-graham) as well as Python software development experience could be a good fit.

osorensen commented 2 years ago

Thanks @yannikschaelte. Once you've updated paper.bib, you can confirm that it works by writing the comments @editorialbot generate pdf and @editorialbot check references in this issue.

osorensen commented 2 years ago

:wave: @nhejazi @GregoryAshton @janfb would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

yannikschaelte commented 2 years ago

@editorialbot generate pdf

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:

yannikschaelte 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

- 10.1126/science.1069492 is OK
- 10.1093/genetics/145.2.505 is OK
- 10.1038/nrg2509 is OK
- 10.1016/j.cels.2016.12.002 is OK
- 10.1214/07-AOS574 is OK
- 10.1002/jae.3950080507 is OK
- 10.1080/10618600.2017.1302882 is OK
- 10.1093/oxfordjournals.molbev.a026091 is OK
- 10.1093/genetics/162.4.2025 is OK
- 10.1073/pnas.0607208104 is OK
- 10.1111/j.1467-9868.2006.00553.x is OK
- 10.1145/3093172.3093233 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1111/2041-210X.12050 is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.1515/sagmb-2012-0069 is OK
- 10.1007/978-3-319-67471-1_8 is OK
- 10.1038/s41467-019-09879-3 is OK
- 10.1371/journal.pcbi.1009149 is OK
- 10.7554/eLife.56265 is OK
- 10.1038/s41586-021-03965-7 is OK
- 10.1063/5.0010764 is OK
- 10.1101/2022.02.10.479738 is OK
- 10.7554/eLife.55665 is OK
- 10.1088/1475-7516/2021/08/027 is OK
- 10.1016/j.compbiomed.2018.10.015 is OK
- 10.1002/eap.2442 is OK
- 10.1101/2021.07.29.454327 is OK
- 10.1214/16-BA1002 is OK
- 10.1214/12-STS406 is OK
- 10.1111/j.1467-9868.2011.01010.x is OK
- 10.5705/ss.202015.0340 is OK
- 10.1016/j.jcp.2020.109999 is OK
- 10.1101/2022.03.18.484896 is OK
- 10.1515/sagmb-2013-0010 is OK
- 10.1093/bioinformatics/btaa397 is OK
- 10.1111/rssb.12312 is OK
- 10.1515/sagmb-2012-0043 is OK
- 10.1111/j.1541-0420.2010.01410.x is OK
- 10.1137/141000671 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1371/journal.pcbi.1008646 is OK
- 10.1093/bioinformatics/btab227 is OK
- 10.1093/bioinformatics/btp619 is OK

MISSING DOIs

- None

INVALID DOIs

- None
nhejazi commented 2 years ago

Thanks for thinking of me for this review, but I am regrettably facing several approaching deadlines and will be unable to provide a review in a timely manner. Hope to participate again in the JOSS review process in the near future.

osorensen commented 2 years ago

Thanks for the quick reply @nhejazi

GregoryAshton commented 2 years ago

Hi @osorensen, my apologies but I am not able to take on the review at the moment due to other responsibilities.

osorensen commented 2 years ago

Thanks for responding, @GregoryAshton

osorensen commented 2 years ago

:wave: @dirmeier @mattpitkin would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

mattpitkin commented 2 years ago

I can take on the review.

osorensen commented 2 years ago

@editorialbot add @mattpitkin as reviewer

editorialbot commented 2 years ago

@mattpitkin added to the reviewers list!

dirmeier commented 2 years ago

Hi, sorry, I don't have much time right now.

osorensen commented 2 years ago

Thanks for your quick response, @dirmeier

osorensen commented 2 years ago

:wave: @blakeaw @hpesonen would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

hpesonen commented 2 years ago

Hi @osorensen. I can do it.

osorensen commented 2 years ago

Thanks @hpesonen!

osorensen commented 2 years ago

@editorialbot add @hpesonen as reviewer

editorialbot commented 2 years ago

@hpesonen added to the reviewers list!

osorensen commented 2 years ago

@editorialbot start review

editorialbot commented 2 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4304.

blakeaw commented 2 years ago

Hi @osorensen, I see the pre-review is closed now and you started the review, so I assume you have enough reviewers already.

osorensen commented 2 years ago

Hi @blakeaw! Yes, we got two reviewers, but it would be excellent to have three. I started the review, and then this issue got automatically closed, but if you're willing to be a reviewer, I would be very happy go add you.

blakeaw commented 2 years ago

@osorensen, okay. Yeah, I'm willing to also be a reviewer if you want to add me as the third.

osorensen commented 2 years ago

Thanks, @blakeaw. I added you over in #4304

yannikschaelte commented 2 years ago

Dear @mattpitkin , @hpesonen , @blakeaw (as well as @osorensen ) thank you very much for reviewing! Looking forward to your feedback in the other issue.