[PRE REVIEW]: ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes #1585

whedon · 2019-07-20T15:27:49Z

Submitting author: @urmi-21 (Urminder Singh)
Repository: https://github.com/urmi-21/ORIS
Version: v1.0
Editor: @csoneson
Reviewers: @jdeligt, @holtgrewe

Author instructions

Thanks for submitting your paper to JOSS @urmi-21. Currently, there isn't an JOSS editor assigned to your paper.

@urmi-21 if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

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The text was updated successfully, but these errors were encountered:

whedon · 2019-07-20T15:27:52Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

whedon · 2019-07-20T15:27:53Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-20T15:27:56Z

PDF failed to compile for issue #1585 with the following error:

Can't find any papers to compile :-(

danielskatz · 2019-07-20T15:28:20Z

@whedon generate pdf

whedon · 2019-07-20T15:28:22Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-20T15:28:27Z

PDF failed to compile for issue #1585 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1585/paper/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:in load'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in open'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:95:in load_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:78:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

danielskatz · 2019-07-20T15:28:55Z

👋 @csoneson - you've been requested as the editor - are you willing to edit this submission?

danielskatz · 2019-07-20T15:33:03Z

👋 @urmi-21 - A fix for the paper compilation issues might be in urmi-21/ORIS#2 Please merge this and see if it fixes the problem, by adding a comment here that says @whedon generate pdf - feel free to iterate

urmi-21 · 2019-07-20T16:26:42Z

@whedon generate pdf

whedon · 2019-07-20T16:26:45Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-20T16:27:05Z

👉 Check article proof 📄 👈

urmi-21 · 2019-07-20T16:32:50Z

@danielskatz Thanks for the suggesting the fix in paper.md. The compiled pdf looks good to me.

danielskatz · 2019-07-20T21:34:15Z

While we are in the process of assigning an editor, you might suggestion some possible reviewers, either from this list (please start at the bottom of the list) or elsewhere, who might be able to review your submission. Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

urmi-21 · 2019-07-20T22:57:57Z

I would like to suggest the following reviewers: @holtgrewe @jdeligt
I hope my submission is appropriate for them to review.

csoneson · 2019-07-21T07:23:23Z

Yes, I can take on this one.

👋 @csoneson - you've been requested as the editor - are you willing to edit this submission?

csoneson · 2019-07-21T07:24:44Z

@holtgrewe, @jdeligt - would you be interested in reviewing this submission for JOSS?

csoneson · 2019-07-21T07:25:07Z

@whedon assign @csoneson as editor

whedon · 2019-07-21T07:25:11Z

OK, the editor is @csoneson

jdeligt · 2019-07-21T11:56:02Z

Count me in.

…

On Sun, 21 Jul 2019, 7:24 pm Charlotte Soneson, ***@***.***> wrote: @holtgrewe <https://github.com/holtgrewe>, @jdeligt <https://github.com/jdeligt> - would you be interested in reviewing this submission for JOSS? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1585?email_source=notifications&email_token=ABMUN72PAK5BEC7CFQF4EOLQAQFMBA5CNFSM4IFO7NW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2N5USY#issuecomment-513530443>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABMUN7ZY2UEMJIRHRX7Z5MLQAQFMBANCNFSM4IFO7NWQ> .

csoneson · 2019-07-21T19:53:11Z

Great @jdeligt - thank you!

csoneson · 2019-07-21T20:49:07Z

@whedon check references

whedon · 2019-07-21T20:49:10Z

Attempting to check references...

whedon · 2019-07-21T20:49:58Z


OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1101/cshperspect.a010108 may be missing for title: Principles and concepts of DNA replication in bacteria, archaea, and eukarya
- https://doi.org/10.1111/j.1365-2958.2005.04622.x may be missing for title: MicroReview: Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes
- https://doi.org/10.1093/bioinformatics/16.6.560 may be missing for title: Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes
- https://doi.org/10.1186/1471-2105-9-79 may be missing for title: Ori-Finder: a web-based system for finding oriC s in unannotated bacterial genomes
- https://doi.org/10.1016/j.biosystems.2011.09.003 may be missing for title: Nucleotide correlation based measure for identifying origin of replication in genomic sequences
- https://doi.org/10.1016/j.biosystems.2011.11.006 may be missing for title: On the origin of three base periodicity in genomes
- https://doi.org/10.1073/pnas.95.7.3720 may be missing for title: Strand compositional asymmetry in bacterial and large viral genomes
- https://doi.org/10.1126/science.272.5262.745 may be missing for title: Origin of replication of Mycoplasma genitalium
- https://doi.org/10.1093/nar/26.10.2286 may be missing for title: Analyzing genomes with cumulative skew diagrams
- https://doi.org/10.1007/s00792-004-0385-4 may be missing for title: Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii
- https://doi.org/10.1155/2005/509646 may be missing for title: Identification of replication origins in archaeal genomes based on the Z-curve method
- https://doi.org/10.3389/fmicb.2014.00482 may be missing for title: Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes
- https://doi.org/10.1002/j.1460-2075.1995.tb07169.x may be missing for title: Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.
- https://doi.org/10.1093/nar/27.23.4636 may be missing for title: Improved microbial gene identification with GLIMMER
- https://doi.org/10.1093/nar/gks990 may be missing for title: DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes
- https://doi.org/10.1111/febs.14150 may be missing for title: Identification and characterization of ARS-like sequences as putative origin (s) of replication in human malaria parasite Plasmodium falciparum

INVALID DOIs

- None

csoneson · 2019-07-21T20:50:56Z

@urmi-21 - while we are recruiting a second reviewer, could you please add DOIs to the references in your paper?

urmi-21 · 2019-07-21T22:35:03Z

@whedon check references

whedon · 2019-07-21T22:35:06Z

Attempting to check references...

whedon · 2019-07-21T22:36:17Z


OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1101/cshperspect.a010108 may be missing for title: Principles and concepts of DNA replication in bacteria, archaea, and eukarya
- https://doi.org/10.1111/j.1365-2958.2005.04622.x may be missing for title: MicroReview: Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes
- https://doi.org/10.1093/bioinformatics/16.6.560 may be missing for title: Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes
- https://doi.org/10.1186/1471-2105-9-79 may be missing for title: Ori-Finder: a web-based system for finding oriC s in unannotated bacterial genomes
- https://doi.org/10.1016/j.biosystems.2011.09.003 may be missing for title: Nucleotide correlation based measure for identifying origin of replication in genomic sequences
- https://doi.org/10.1016/j.biosystems.2011.11.006 may be missing for title: On the origin of three base periodicity in genomes
- https://doi.org/10.1073/pnas.95.7.3720 may be missing for title: Strand compositional asymmetry in bacterial and large viral genomes
- https://doi.org/10.1126/science.272.5262.745 may be missing for title: Origin of replication of Mycoplasma genitalium
- https://doi.org/10.1093/nar/26.10.2286 may be missing for title: Analyzing genomes with cumulative skew diagrams
- https://doi.org/10.1007/s00792-004-0385-4 may be missing for title: Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii
- https://doi.org/10.1155/2005/509646 may be missing for title: Identification of replication origins in archaeal genomes based on the Z-curve method
- https://doi.org/10.3389/fmicb.2014.00482 may be missing for title: Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes
- https://doi.org/10.1002/j.1460-2075.1995.tb07169.x may be missing for title: Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.
- https://doi.org/10.1093/nar/27.23.4636 may be missing for title: Improved microbial gene identification with GLIMMER
- https://doi.org/10.1093/nar/gks990 may be missing for title: DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes
- https://doi.org/10.1111/febs.14150 may be missing for title: Identification and characterization of ARS-like sequences as putative origin (s) of replication in human malaria parasite Plasmodium falciparum

INVALID DOIs

- None

urmi-21 · 2019-07-21T22:37:44Z

@whedon generate pdf

whedon · 2019-07-21T22:37:46Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-21T22:38:07Z

👉 Check article proof 📄 👈

urmi-21 · 2019-07-21T22:38:12Z

@whedon check references

whedon · 2019-07-21T22:38:14Z

Attempting to check references...

whedon · 2019-07-21T22:38:29Z


OK DOIs

- 10.1201/9781315815015 is OK
- 10.1101/cshperspect.a010108 is OK
- 10.1111/j.1365-2958.2005.04622.x is OK
- 10.1093/bioinformatics/16.6.560 is OK
- 10.1186/1471-2105-9-79 is OK
- 10.1016/j.biosystems.2011.09.003 is OK
- 10.1016/j.biosystems.2011.11.006 is OK
- 10.1111/febs.14150 is OK

MISSING DOIs

- None

INVALID DOIs

- None

urmi-21 · 2019-07-21T22:41:58Z

@csoneson Hi, I've added the DOIs to the references. Thanks.

holtgrewe · 2019-07-22T06:14:33Z

@csoneson sure can do ;)

csoneson · 2019-07-22T13:40:21Z

@holtgrewe great, thanks! I'm going to open the review issue, and then we'll head over there for the actual review

csoneson · 2019-07-22T13:41:06Z

@whedon assign @jdeligt as reviewer

whedon · 2019-07-22T13:41:11Z

OK, the reviewer is @jdeligt

csoneson · 2019-07-22T13:41:23Z

@whedon add @holtgrewe as reviewer

whedon · 2019-07-22T13:41:29Z

OK, @holtgrewe is now a reviewer

csoneson · 2019-07-22T13:41:45Z

@whedon start review

whedon · 2019-07-22T13:41:50Z

OK, I've started the review over in #1589. Feel free to close this issue now!

whedon added the pre-review label Jul 20, 2019

whedon added Java TeX labels Jul 20, 2019

whedon assigned csoneson Jul 21, 2019

whedon unassigned csoneson Jul 22, 2019

whedon assigned csoneson and jdeligt Jul 22, 2019

whedon assigned csoneson, holtgrewe and jdeligt and unassigned csoneson and jdeligt Jul 22, 2019

csoneson closed this as completed Jul 22, 2019

[PRE REVIEW]: ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes #1585

[PRE REVIEW]: ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes #1585

Comments

whedon commented Jul 20, 2019 • edited

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whedon commented Jul 20, 2019 •

edited