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Paper: Diving into Human cell with bioservices and cellnopt (T. Cokelaer) #38

Closed cokelaer closed 9 years ago

cokelaer commented 10 years ago

This is a draft version of the paper "Diving into Human cell with bioservices and cellnopt", together with the images that makes the paper.

Best Thomas

NelleV commented 10 years ago

Thank you for the submission! The review process should start soon. Nelle

cokelaer commented 10 years ago

Dear Nelle,

Is there still a change to ammend the document and do another pull request ? If so until when ?

Best Thomas

On Wed 20 Aug 2014 23:37:02 BST, Varoquaux wrote:

Thank you for the submission! The review process should start soon. Nelle

— Reply to this email directly or view it on GitHub https://github.com/euroscipy/euroscipy_proceedings/pull/38#issuecomment-52855040.

pdebuyl commented 10 years ago

You can push minor changes to your repository. The pull request will be automatically updated.

You shouldn't make important changes until the first reviews are in (except if you do them within the next few hours so that they'll be included already).

cokelaer commented 10 years ago

This new version of the paper is similar to the previous one with a few differences : (i) typo fixes, (ii) missing references added (iii) some rewriting in the conclusions and discussions (iv) and more meaningful title but nothing really new. I do understand that the previous version is most probably in the reviewers' hands already. We'll incorporate those changes during the next stage of the review. Best. Thomas

ctb commented 10 years ago

I'll review this paper.

NelleV commented 10 years ago

I'll also be reviewing this paper. Do you mind wrapping up the lines to 80 char? The paper will then be much easier to review. Thanks, N

pdebuyl commented 10 years ago

reminder to @ctb and @NelleV

ctb commented 10 years ago

Review complete. All of my comments were minor; overall, I find the paper is well written and provides good insight not only into what the software packages do (computationally and with biological motivation) but why this approach was chosen. Great stuff.

NelleV commented 10 years ago

I'm deeply sorry for my late review…

I left some details remark in line notes. Overall, you did a very good job at explaining what bioservices and cellopnt are, thought there are typos and small language mistakes. I think @ctb and I underlined most of them, but it is worth reading thoroughly the paper again to make sure we didn't let anything slip.

I recommend this paper for publication after the remarks have been adressed. Thanks, Nelle

cokelaer commented 10 years ago

Thanks for the comments and suggestions. Here is the revised version of the paper taking into account comments from the reviewers.

Last version being 64df187ad78bb0d871e896a21b26f16d50675097

Best Thomas

cokelaer commented 10 years ago

Dear all, I've updated the final version of the paper with minor typos and slight updates. I'm not sure about the next step. Everything is in my forked repository of euroscipy. Shall I do another pull request ? Thomas

ctb commented 10 years ago

The pull request has been updated with your changes. But I don't know if we do another round of review or what?

On Fri, Oct 03, 2014 at 07:47:30AM -0700, Thomas Cokelaer wrote:

Dear all, I've updated the final version of the paper with minor typos and slight updates. I'm not sure about the next step. Everything is in my forked repository of euroscipy. Shall I do another pull request ? Thomas

Reply to this email directly or view it on GitHub:

https://github.com/euroscipy/euroscipy_proceedings/pull/38#issuecomment-57805925

C. Titus Brown, ctb@msu.edu

NelleV commented 10 years ago

The pull request has been updated with your changes. But I don't know if we do another round of review or what?

Yes please! If you think the paper should be accepted in this form, just say so in the review (and we will merge). I'll do mine either today or tomorrow.

On Fri, Oct 03, 2014 at 07:47:30AM -0700, Thomas Cokelaer wrote:

Dear all, I've updated the final version of the paper with minor typos and slight updates. I'm not sure about the next step. Everything is in my forked repository of euroscipy. Shall I do another pull request ? Thomas

Reply to this email directly or view it on GitHub:

https://github.com/euroscipy/euroscipy_proceedings/pull/38#issuecomment-57805925

C. Titus Brown, ctb@msu.edu

— Reply to this email directly or view it on GitHub https://github.com/euroscipy/euroscipy_proceedings/pull/38#issuecomment-57806107 .

cokelaer commented 10 years ago

FYI except from typos here are the main differences:

ctb commented 10 years ago

I am fine with the revisions!

cokelaer commented 10 years ago

Is there anything else to be done on my side for now ? Best

cokelaer commented 10 years ago

committed and pushed the typos.

pdebuyl commented 10 years ago

@NelleV is the current version ok?

cokelaer commented 10 years ago

Yes. all comments were taken into account. Let me know the next step. Thanks

pdebuyl commented 10 years ago

Dear Thomas,

Thank you for the notice. My request was addressed to Nelle but I see that she already confirmed acceptance modulo the fixes that you have addressed. There is no further action needed from you. The paper will be merged but I will first review the global layout of the proceedings.

Thanks to all for the paper and reviews!

Regards,

Pierre