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opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
https://opencobra.github.io/cobratoolbox
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Bug in updateCobraToolbox.m #412

Closed acalapez closed 7 years ago

acalapez commented 7 years ago

In lines 38,39,51,52 of updateCobraToolbox.m should be = instead of == This prevents updating CTB from matlab. Correcting the code makes it work but still can't update because it complains that there are non commit changes.

I hereby confirm that I have:

laurentheirendt commented 7 years ago

Thanks @acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes - and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools.

If you however want to update (:warning: your changes will be lost), you can do the following from the terminal:

$ git stash
$ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

rmtfleming commented 7 years ago

I recommend to use MATLAB.devTools https://github.com/opencobra/MATLAB.devTools. It allows you to focus more on coding and less on the internal mechanics of git.

On 4 May 2017 at 07:42, Laurent Heirendt notifications@github.com wrote:

Closed #412 https://github.com/opencobra/cobratoolbox/issues/412.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#event-1068365837, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOoQgn5V2SxVgaa12JcwyDlfEBhuHks5r2WUpgaJpZM4NQH0r .

-- --

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

acalapez commented 7 years ago

Hi

Thank you so much for your reply. I am familiar with git. I have not made any pull requests because I am not aware of your policies regarding (outside) contributions and didn't want to mess with your work.

I did circumvent the issue by writing an "updateCobraToolboxFix.m" outside the git repository folder (but still on matlab path) and using it to update. There were a few update issues in the development branch but since I'm was trying to make a model work with the code in master I didn't recorded them (I can check that during the weekend if you wish).

If I may bother you a little more, I am trying to optimize a yeast reaction model written in SMBL that was delivered to me "as is". I am getting a number of warnings concerning an entry "sgd" that supposedly reports to some data in the EMBL database. I haven't been able to check exactly what is it but apparently some reactions are left out. I haven't reported this because I am not sure if it qualifies as a bug. Probably it qualifies as a "unsupported" entry. Are you aware of anything like this and if so, how to solve it? (e.g. alternative SMBL readers)

Thank you in advance...

Looking forward for the new updates

AC

On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt notifications@github.com wrote:

Thanks @acalapez https://github.com/acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes - and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools https://github.com/opencobra/MATLAB.devTools.

If you however want to update (⚠️ your changes will be lost), you can do the following from the terminal:

$ git stash $ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299100860, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-OW84-Vgjd-hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r .

rmtfleming commented 7 years ago

Hi AC,

below is a recent request for contributions.

A function very similar to your update cobra toolbox function is also in the devel branch at the moment and undergoing testing. We want to make it as easy as possible for people to contribute and get others contributions.

As for the yeast model io issue, I am not sure. If you are using all of the latest cobra toolbox functions then it could be a bug in our code, or the code for SBML import or it could be due to misspecification of the .xml file somehow. We put a lot of effort into updating the io functionality with Sarah. If you post here the detailed warnings/errors then we can look at them, but we are not responsible if it is a misspecification of the .xml file.

Regards,

Ronan

==================

Dear user and developer of The COBRA Toolbox,

over the last years, the developer community has assembled a comprehensive suite of COBRA methods and algorithms, tutorials, and tests. As the code base grew larger in size, the code complexity inevitably increased. In order to redress this situation, we launched a significant effort in October 2016 to improve the user friendliness and accessibility through easy-to-follow tutorials and documentation. We set up a continuous integration (CI) server that is testing automatically every change in the code in order to ensure high quality, stable code, and ultimately, guarantee reproducibility of results.

The developer community has been very active over the last months. Nonetheless, The COBRA Toolbox cannot be turned into a comprehensive professional code base for constraint-based reconstruction and analysis without the contributions of the community. That is the reason why we reach out to you - help your community grow!

We aim to submit a publication to Nature Protocols by the end of June 2017 that will highlight the user friendliness, new features, and improved quality of The COBRA Toolbox. In order to overachieve on this goal, we need your support with code contributions, elaborating tutorials, writing tests for existing code, and feedback.

Please note that while MATLAB is used as the main language within The COBRA Toolbox, we already have selectively interfaced to some algorithms in other languages, including perl, python, C, julia and many binaries. We welcome the computational language agnostic, open source development of all forms of COBRA code and welcome support to integrate with complementary tools, including within the broader https://opencobra.github.io/community effort.

You will find instructions on how to contribute on www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. As The COBRA Toolbox is tracked using the git versioning system, you might feel overwhelmed with submitting your contribution as a pull request (PR). The newly released MATLAB.devTools (www.github.com/opencobra/ http://www.github.com/opencobra/MATLAB.devTools) that we developed specifically for this project, allows you to easily submit your contribution from within MATLAB. We look forward to hearing from you and reading your pull request! If you need help, please feel free to post in our forum on www.groups.google.com/forum/#!forum/cobra-toolbox

In order to honor your contribution, we will evaluate your contributions, since the publication of the v2 protocol June 2017, based on the following weighted criteria as a guideline:

25%: Number of contributed tutorials (.mlx format) / Total number of tutorials

15%: Number of commits / Total number of commits (square root)

15%: Number of submitted & merged PRs / Total number of submitted & merged PRs

15%: Number of support messages on forum & issues / Total number of support messages on forum & issues

15%: Number of lines added / Total number of lines added

15%: Number of lines removed / Total number of lines removed

With a significant contribution based on the weighting above, your authorship on the publication will be assured. Principal investigators of the most significantly contributing individuals will also be added to the senior authors list, unless they elect otherwise. The order of authors on the publication will be determined based on the contribution guideline. The basis for this decision will be transparently disseminated via www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. Please note that the last COBRA Toolbox protocol paper (doi:10.1038/nprot.2011.308) has been cited in excess of 700 times, illustrating the breadth of our community.

Please also note the citation guideline for users of The COBRA Toolbox, where we ask people to cite the original paper that first reported a new algorithm as well as the appropriate COBRA Toolbox paper, so that we ensure creation and dissemination are both credited.

We are looking forward to your contributions!

Regards,

Dr. Ronan M.T. Fleming,

Lead COBRA Toolbox developer (since December 2015).

================

On 4 May 2017 at 17:10, acalapez notifications@github.com wrote:

Hi

Thank you so much for your reply. I am familiar with git. I have not made any pull requests because I am not aware of your policies regarding (outside) contributions and didn't want to mess with your work.

I did circumvent the issue by writing an "updateCobraToolboxFix.m" outside the git repository folder (but still on matlab path) and using it to update. There were a few update issues in the development branch but since I'm was trying to make a model work with the code in master I didn't recorded them (I can check that during the weekend if you wish).

If I may bother you a little more, I am trying to optimize a yeast reaction model written in SMBL that was delivered to me "as is". I am getting a number of warnings concerning an entry "sgd" that supposedly reports to some data in the EMBL database. I haven't been able to check exactly what is it but apparently some reactions are left out. I haven't reported this because I am not sure if it qualifies as a bug. Probably it qualifies as a "unsupported" entry. Are you aware of anything like this and if so, how to solve it? (e.g. alternative SMBL readers)

Thank you in advance...

Looking forward for the new updates

AC

On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt <notifications@github.com

wrote:

Thanks @acalapez https://github.com/acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes - and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools https://github.com/opencobra/MATLAB.devTools.

If you however want to update (⚠️ your changes will be lost), you can do the following from the terminal:

$ git stash $ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299100860, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-OW84-Vgjd- hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299214632, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOmxnUN1hx-WFI-Y7zFa9Ot2mGf0Pks5r2epmgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

acalapez commented 7 years ago

Hi Ronan

I'm working primarily with ADMM based optimization. This is a kind of side-project someone asked me to look into. Still, I'd be happy to get involved (at least as much as I could fit into my schedule). In the weekend I'll take a look at the link you just sent and see how I may contribute.

Regarding the SMBL issue, I'll try to figure it out. Indeed, I'm suspecting some kind of misspecification (or lack of experience with CTB on my side), and for this reason I find it premature to post it as an issue. I can still send the xml and the matlab (2016b) output if you tell me where (or to whom) to, if I find no way to circumvent the issue.

I'll keep you posted (or someone else, if you prefer) as to my availability to contribute.

Best regards

AC

On Thu, May 4, 2017 at 5:03 PM, Ronan M.T. Fleming <notifications@github.com

wrote:

Hi AC,

below is a recent request for contributions.

A function very similar to your update cobra toolbox function is also in the devel branch at the moment and undergoing testing. We want to make it as easy as possible for people to contribute and get others contributions.

As for the yeast model io issue, I am not sure. If you are using all of the latest cobra toolbox functions then it could be a bug in our code, or the code for SBML import or it could be due to misspecification of the .xml file somehow. We put a lot of effort into updating the io functionality with Sarah. If you post here the detailed warnings/errors then we can look at them, but we are not responsible if it is a misspecification of the .xml file.

Regards,

Ronan

==================

Dear user and developer of The COBRA Toolbox,

over the last years, the developer community has assembled a comprehensive suite of COBRA methods and algorithms, tutorials, and tests. As the code base grew larger in size, the code complexity inevitably increased. In order to redress this situation, we launched a significant effort in October 2016 to improve the user friendliness and accessibility through easy-to-follow tutorials and documentation. We set up a continuous integration (CI) server that is testing automatically every change in the code in order to ensure high quality, stable code, and ultimately, guarantee reproducibility of results.

The developer community has been very active over the last months. Nonetheless, The COBRA Toolbox cannot be turned into a comprehensive professional code base for constraint-based reconstruction and analysis without the contributions of the community. That is the reason why we reach out to you - help your community grow!

We aim to submit a publication to Nature Protocols by the end of June 2017 that will highlight the user friendliness, new features, and improved quality of The COBRA Toolbox. In order to overachieve on this goal, we need your support with code contributions, elaborating tutorials, writing tests for existing code, and feedback.

Please note that while MATLAB is used as the main language within The COBRA Toolbox, we already have selectively interfaced to some algorithms in other languages, including perl, python, C, julia and many binaries. We welcome the computational language agnostic, open source development of all forms of COBRA code and welcome support to integrate with complementary tools, including within the broader https://opencobra.github.io/community effort.

You will find instructions on how to contribute on www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. As The COBRA Toolbox is tracked using the git versioning system, you might feel overwhelmed with submitting your contribution as a pull request (PR). The newly released MATLAB.devTools (www.github.com/opencobra/ http://www.github.com/opencobra/MATLAB.devTools) that we developed specifically for this project, allows you to easily submit your contribution from within MATLAB. We look forward to hearing from you and reading your pull request! If you need help, please feel free to post in our forum on www.groups.google.com/forum/#!forum/cobra-toolbox

In order to honor your contribution, we will evaluate your contributions, since the publication of the v2 protocol June 2017, based on the following weighted criteria as a guideline:

25%: Number of contributed tutorials (.mlx format) / Total number of tutorials

15%: Number of commits / Total number of commits (square root)

15%: Number of submitted & merged PRs / Total number of submitted & merged PRs

15%: Number of support messages on forum & issues / Total number of support messages on forum & issues

15%: Number of lines added / Total number of lines added

15%: Number of lines removed / Total number of lines removed

With a significant contribution based on the weighting above, your authorship on the publication will be assured. Principal investigators of the most significantly contributing individuals will also be added to the senior authors list, unless they elect otherwise. The order of authors on the publication will be determined based on the contribution guideline. The basis for this decision will be transparently disseminated via www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. Please note that the last COBRA Toolbox protocol paper (doi:10.1038/nprot.2011.308) has been cited in excess of 700 times, illustrating the breadth of our community.

Please also note the citation guideline for users of The COBRA Toolbox, where we ask people to cite the original paper that first reported a new algorithm as well as the appropriate COBRA Toolbox paper, so that we ensure creation and dissemination are both credited.

We are looking forward to your contributions!

Regards,

Dr. Ronan M.T. Fleming,

Lead COBRA Toolbox developer (since December 2015).

================

On 4 May 2017 at 17:10, acalapez notifications@github.com wrote:

Hi

Thank you so much for your reply. I am familiar with git. I have not made any pull requests because I am not aware of your policies regarding (outside) contributions and didn't want to mess with your work.

I did circumvent the issue by writing an "updateCobraToolboxFix.m" outside the git repository folder (but still on matlab path) and using it to update. There were a few update issues in the development branch but since I'm was trying to make a model work with the code in master I didn't recorded them (I can check that during the weekend if you wish).

If I may bother you a little more, I am trying to optimize a yeast reaction model written in SMBL that was delivered to me "as is". I am getting a number of warnings concerning an entry "sgd" that supposedly reports to some data in the EMBL database. I haven't been able to check exactly what is it but apparently some reactions are left out. I haven't reported this because I am not sure if it qualifies as a bug. Probably it qualifies as a "unsupported" entry. Are you aware of anything like this and if so, how to solve it? (e.g. alternative SMBL readers)

Thank you in advance...

Looking forward for the new updates

AC

On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt < notifications@github.com

wrote:

Thanks @acalapez https://github.com/acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes - and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools <https://github.com/opencobra/MATLAB.devTools .

If you however want to update (⚠️ your changes will be lost), you can do the following from the terminal:

$ git stash $ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299100860, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-OW84-Vgjd- hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299214632, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOmxnUN1hx-WFI- Y7zFa9Ot2mGf0Pks5r2epmgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299231118, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-NYrkJOnA2YUPjHmSN3k12MIZ4cks5r2fbJgaJpZM4NQH0r .

rmtfleming commented 7 years ago

Hi AC,

try http://sbml.org/Facilities/Validator/ this with your xml file.

Regards,

Ronan

On 4 May 2017 at 19:01, acalapez notifications@github.com wrote:

Hi Ronan

I'm working primarily with ADMM based optimization. This is a kind of side-project someone asked me to look into. Still, I'd be happy to get involved (at least as much as I could fit into my schedule). In the weekend I'll take a look at the link you just sent and see how I may contribute.

Regarding the SMBL issue, I'll try to figure it out. Indeed, I'm suspecting some kind of misspecification (or lack of experience with CTB on my side), and for this reason I find it premature to post it as an issue. I can still send the xml and the matlab (2016b) output if you tell me where (or to whom) to, if I find no way to circumvent the issue.

I'll keep you posted (or someone else, if you prefer) as to my availability to contribute.

Best regards

AC

On Thu, May 4, 2017 at 5:03 PM, Ronan M.T. Fleming < notifications@github.com

wrote:

Hi AC,

below is a recent request for contributions.

A function very similar to your update cobra toolbox function is also in the devel branch at the moment and undergoing testing. We want to make it as easy as possible for people to contribute and get others contributions.

As for the yeast model io issue, I am not sure. If you are using all of the latest cobra toolbox functions then it could be a bug in our code, or the code for SBML import or it could be due to misspecification of the .xml file somehow. We put a lot of effort into updating the io functionality with Sarah. If you post here the detailed warnings/errors then we can look at them, but we are not responsible if it is a misspecification of the .xml file.

Regards,

Ronan

==================

Dear user and developer of The COBRA Toolbox,

over the last years, the developer community has assembled a comprehensive suite of COBRA methods and algorithms, tutorials, and tests. As the code base grew larger in size, the code complexity inevitably increased. In order to redress this situation, we launched a significant effort in October 2016 to improve the user friendliness and accessibility through easy-to-follow tutorials and documentation. We set up a continuous integration (CI) server that is testing automatically every change in the code in order to ensure high quality, stable code, and ultimately, guarantee reproducibility of results.

The developer community has been very active over the last months. Nonetheless, The COBRA Toolbox cannot be turned into a comprehensive professional code base for constraint-based reconstruction and analysis without the contributions of the community. That is the reason why we reach out to you - help your community grow!

We aim to submit a publication to Nature Protocols by the end of June 2017 that will highlight the user friendliness, new features, and improved quality of The COBRA Toolbox. In order to overachieve on this goal, we need your support with code contributions, elaborating tutorials, writing tests for existing code, and feedback.

Please note that while MATLAB is used as the main language within The COBRA Toolbox, we already have selectively interfaced to some algorithms in other languages, including perl, python, C, julia and many binaries. We welcome the computational language agnostic, open source development of all forms of COBRA code and welcome support to integrate with complementary tools, including within the broader https://opencobra.github.io/community effort.

You will find instructions on how to contribute on www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. As The COBRA Toolbox is tracked using the git versioning system, you might feel overwhelmed with submitting your contribution as a pull request (PR). The newly released MATLAB.devTools (www.github.com/opencobra/ http://www.github.com/opencobra/MATLAB.devTools) that we developed specifically for this project, allows you to easily submit your contribution from within MATLAB. We look forward to hearing from you and reading your pull request! If you need help, please feel free to post in our forum on www.groups.google.com/forum/#!forum/cobra-toolbox

In order to honor your contribution, we will evaluate your contributions, since the publication of the v2 protocol June 2017, based on the following weighted criteria as a guideline:

25%: Number of contributed tutorials (.mlx format) / Total number of tutorials

15%: Number of commits / Total number of commits (square root)

15%: Number of submitted & merged PRs / Total number of submitted & merged PRs

15%: Number of support messages on forum & issues / Total number of support messages on forum & issues

15%: Number of lines added / Total number of lines added

15%: Number of lines removed / Total number of lines removed

With a significant contribution based on the weighting above, your authorship on the publication will be assured. Principal investigators of the most significantly contributing individuals will also be added to the senior authors list, unless they elect otherwise. The order of authors on the publication will be determined based on the contribution guideline. The basis for this decision will be transparently disseminated via www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. Please note that the last

COBRA Toolbox protocol paper (doi:10.1038/nprot.2011.308) has been cited in excess of 700 times, illustrating the breadth of our community.

Please also note the citation guideline for users of The COBRA Toolbox, where we ask people to cite the original paper that first reported a new algorithm as well as the appropriate COBRA Toolbox paper, so that we ensure creation and dissemination are both credited.

We are looking forward to your contributions!

Regards,

Dr. Ronan M.T. Fleming,

Lead COBRA Toolbox developer (since December 2015).

================

On 4 May 2017 at 17:10, acalapez notifications@github.com wrote:

Hi

Thank you so much for your reply. I am familiar with git. I have not made any pull requests because I am not aware of your policies regarding (outside) contributions and didn't want to mess with your work.

I did circumvent the issue by writing an "updateCobraToolboxFix.m" outside the git repository folder (but still on matlab path) and using it to update. There were a few update issues in the development branch but since I'm was trying to make a model work with the code in master I didn't recorded them (I can check that during the weekend if you wish).

If I may bother you a little more, I am trying to optimize a yeast reaction model written in SMBL that was delivered to me "as is". I am getting a number of warnings concerning an entry "sgd" that supposedly reports to some data in the EMBL database. I haven't been able to check exactly what is it but apparently some reactions are left out. I haven't reported this because I am not sure if it qualifies as a bug. Probably it qualifies as a "unsupported" entry. Are you aware of anything like this and if so, how to solve it? (e.g. alternative SMBL readers)

Thank you in advance...

Looking forward for the new updates

AC

On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt < notifications@github.com

wrote:

Thanks @acalapez https://github.com/acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes - and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools <https://github.com/opencobra/ MATLAB.devTools .

If you however want to update (⚠️ your changes will be lost), you can do the following from the terminal:

$ git stash $ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299100860 <29%2091%2000%20860>>, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-OW84-Vgjd- hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299214632 <29%2092%2014%20632>>, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOmxnUN1hx-WFI- Y7zFa9Ot2mGf0Pks5r2epmgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <621%20175%20112> <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299231118, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2- NYrkJOnA2YUPjHmSN3k12MIZ4cks5r2fbJgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299246938, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOhOKUSqww8rGcR-VRyuVHUmpzClHks5r2gRegaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

rmtfleming commented 7 years ago

https://github.com/acalapez is who?

On 4 May 2017 at 19:49, Ronan M.T. Fleming ronan.mt.fleming@gmail.com wrote:

Hi AC,

try http://sbml.org/Facilities/Validator/ this with your xml file.

Regards,

Ronan

On 4 May 2017 at 19:01, acalapez notifications@github.com wrote:

Hi Ronan

I'm working primarily with ADMM based optimization. This is a kind of side-project someone asked me to look into. Still, I'd be happy to get involved (at least as much as I could fit into my schedule). In the weekend I'll take a look at the link you just sent and see how I may contribute.

Regarding the SMBL issue, I'll try to figure it out. Indeed, I'm suspecting some kind of misspecification (or lack of experience with CTB on my side), and for this reason I find it premature to post it as an issue. I can still send the xml and the matlab (2016b) output if you tell me where (or to whom) to, if I find no way to circumvent the issue.

I'll keep you posted (or someone else, if you prefer) as to my availability to contribute.

Best regards

AC

On Thu, May 4, 2017 at 5:03 PM, Ronan M.T. Fleming < notifications@github.com

wrote:

Hi AC,

below is a recent request for contributions.

A function very similar to your update cobra toolbox function is also in the devel branch at the moment and undergoing testing. We want to make it as easy as possible for people to contribute and get others contributions.

As for the yeast model io issue, I am not sure. If you are using all of the latest cobra toolbox functions then it could be a bug in our code, or the code for SBML import or it could be due to misspecification of the .xml file somehow. We put a lot of effort into updating the io functionality with Sarah. If you post here the detailed warnings/errors then we can look at them, but we are not responsible if it is a misspecification of the .xml file.

Regards,

Ronan

==================

Dear user and developer of The COBRA Toolbox,

over the last years, the developer community has assembled a comprehensive suite of COBRA methods and algorithms, tutorials, and tests. As the code base grew larger in size, the code complexity inevitably increased. In order to redress this situation, we launched a significant effort in October 2016 to improve the user friendliness and accessibility through easy-to-follow tutorials and documentation. We set up a continuous integration (CI) server that is testing automatically every change in the code in order to ensure high quality, stable code, and ultimately, guarantee reproducibility of results.

The developer community has been very active over the last months. Nonetheless, The COBRA Toolbox cannot be turned into a comprehensive professional code base for constraint-based reconstruction and analysis without the contributions of the community. That is the reason why we reach out to you - help your community grow!

We aim to submit a publication to Nature Protocols by the end of June 2017 that will highlight the user friendliness, new features, and improved quality of The COBRA Toolbox. In order to overachieve on this goal, we need your support with code contributions, elaborating tutorials, writing tests for existing code, and feedback.

Please note that while MATLAB is used as the main language within The COBRA Toolbox, we already have selectively interfaced to some algorithms in other languages, including perl, python, C, julia and many binaries. We welcome the computational language agnostic, open source development of all forms of COBRA code and welcome support to integrate with complementary tools, including within the broader https://opencobra.github.io/community effort.

You will find instructions on how to contribute on www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. As The COBRA Toolbox is tracked using the git versioning system, you might feel overwhelmed with submitting your contribution as a pull request (PR). The newly released MATLAB.devTools (www.github.com/opencobra/ http://www.github.com/opencobra/MATLAB.devTools) that we developed specifically for this project, allows you to easily submit your contribution from within MATLAB. We look forward to hearing from you and reading your pull request! If you need help, please feel free to post in our forum on www.groups.google.com/forum/#!forum/cobra-toolbox

In order to honor your contribution, we will evaluate your contributions, since the publication of the v2 protocol June 2017, based on the following weighted criteria as a guideline:

25%: Number of contributed tutorials (.mlx format) / Total number of tutorials

15%: Number of commits / Total number of commits (square root)

15%: Number of submitted & merged PRs / Total number of submitted & merged PRs

15%: Number of support messages on forum & issues / Total number of support messages on forum & issues

15%: Number of lines added / Total number of lines added

15%: Number of lines removed / Total number of lines removed

With a significant contribution based on the weighting above, your authorship on the publication will be assured. Principal investigators of the most significantly contributing individuals will also be added to the senior authors list, unless they elect otherwise. The order of authors on the publication will be determined based on the contribution guideline. The basis for this decision will be transparently disseminated via www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. Please note that the last

COBRA Toolbox protocol paper (doi:10.1038/nprot.2011.308) has been cited in excess of 700 times, illustrating the breadth of our community.

Please also note the citation guideline for users of The COBRA Toolbox, where we ask people to cite the original paper that first reported a new algorithm as well as the appropriate COBRA Toolbox paper, so that we ensure creation and dissemination are both credited.

We are looking forward to your contributions!

Regards,

Dr. Ronan M.T. Fleming,

Lead COBRA Toolbox developer (since December 2015).

================

On 4 May 2017 at 17:10, acalapez notifications@github.com wrote:

Hi

Thank you so much for your reply. I am familiar with git. I have not made any pull requests because I am not aware of your policies regarding (outside) contributions and didn't want to mess with your work.

I did circumvent the issue by writing an "updateCobraToolboxFix.m" outside the git repository folder (but still on matlab path) and using it to update. There were a few update issues in the development branch but since I'm was trying to make a model work with the code in master I didn't recorded them (I can check that during the weekend if you wish).

If I may bother you a little more, I am trying to optimize a yeast reaction model written in SMBL that was delivered to me "as is". I am getting a number of warnings concerning an entry "sgd" that supposedly reports to some data in the EMBL database. I haven't been able to check exactly what is it but apparently some reactions are left out. I haven't reported this because I am not sure if it qualifies as a bug. Probably it qualifies as a "unsupported" entry. Are you aware of anything like this and if so, how to solve it? (e.g. alternative SMBL readers)

Thank you in advance...

Looking forward for the new updates

AC

On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt < notifications@github.com

wrote:

Thanks @acalapez https://github.com/acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes - and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools <https://github.com/opencobra/ MATLAB.devTools .

If you however want to update (⚠️ your changes will be lost), you can do the following from the terminal:

$ git stash $ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299100860 <29%2091%2000%20860>>, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-OW84-Vgjd- hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299214632 <29%2092%2014%20632>>, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOmxnUN1hx-WFI- Y7zFa9Ot2mGf0Pks5r2epmgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <621%20175%20112> <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuec omment-299231118, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-NYr kJOnA2YUPjHmSN3k12MIZ4cks5r2fbJgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299246938, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOhOKUSqww8rGcR-VRyuVHUmpzClHks5r2gRegaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

acalapez commented 7 years ago

Hi

Thanks. Will do.

https://github.com/acalapez is my (newly created) personal account at github.

Regards

AC

On Thu, May 4, 2017 at 6:53 PM, Ronan M.T. Fleming <notifications@github.com

wrote:

https://github.com/acalapez is who?

On 4 May 2017 at 19:49, Ronan M.T. Fleming ronan.mt.fleming@gmail.com wrote:

Hi AC,

try http://sbml.org/Facilities/Validator/ this with your xml file.

Regards,

Ronan

On 4 May 2017 at 19:01, acalapez notifications@github.com wrote:

Hi Ronan

I'm working primarily with ADMM based optimization. This is a kind of side-project someone asked me to look into. Still, I'd be happy to get involved (at least as much as I could fit into my schedule). In the weekend I'll take a look at the link you just sent and see how I may contribute.

Regarding the SMBL issue, I'll try to figure it out. Indeed, I'm suspecting some kind of misspecification (or lack of experience with CTB on my side), and for this reason I find it premature to post it as an issue. I can still send the xml and the matlab (2016b) output if you tell me where (or to whom) to, if I find no way to circumvent the issue.

I'll keep you posted (or someone else, if you prefer) as to my availability to contribute.

Best regards

AC

On Thu, May 4, 2017 at 5:03 PM, Ronan M.T. Fleming < notifications@github.com

wrote:

Hi AC,

below is a recent request for contributions.

A function very similar to your update cobra toolbox function is also in the devel branch at the moment and undergoing testing. We want to make it as easy as possible for people to contribute and get others contributions.

As for the yeast model io issue, I am not sure. If you are using all of the latest cobra toolbox functions then it could be a bug in our code, or the code for SBML import or it could be due to misspecification of the .xml file somehow. We put a lot of effort into updating the io functionality with Sarah. If you post here the detailed warnings/errors then we can look at them, but we are not responsible if it is a misspecification of the .xml file.

Regards,

Ronan

==================

Dear user and developer of The COBRA Toolbox,

over the last years, the developer community has assembled a comprehensive suite of COBRA methods and algorithms, tutorials, and tests. As the code base grew larger in size, the code complexity inevitably increased. In order to redress this situation, we launched a significant effort in October 2016 to improve the user friendliness and accessibility through easy-to-follow tutorials and documentation. We set up a continuous integration (CI) server that is testing automatically every change in the code in order to ensure high quality, stable code, and ultimately, guarantee reproducibility of results.

The developer community has been very active over the last months. Nonetheless, The COBRA Toolbox cannot be turned into a comprehensive professional code base for constraint-based reconstruction and analysis without the contributions of the community. That is the reason why we reach out to you - help your community grow!

We aim to submit a publication to Nature Protocols by the end of June 2017 that will highlight the user friendliness, new features, and improved quality of The COBRA Toolbox. In order to overachieve on this goal, we need your support with code contributions, elaborating tutorials, writing tests for existing code, and feedback.

Please note that while MATLAB is used as the main language within The COBRA Toolbox, we already have selectively interfaced to some algorithms in other languages, including perl, python, C, julia and many binaries. We welcome the computational language agnostic, open source development of all forms of COBRA code and welcome support to integrate with complementary tools, including within the broader https://opencobra.github.io/community effort.

You will find instructions on how to contribute on www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. As The COBRA Toolbox is tracked using the git versioning system, you might feel overwhelmed with submitting your contribution as a pull request (PR). The newly released MATLAB.devTools (www.github.com/opencobra/ http://www.github.com/opencobra/MATLAB.devTools) that we developed specifically for this project, allows you to easily submit your contribution from within MATLAB. We look forward to hearing from you and reading your pull request! If you need help, please feel free to post in our forum on www.groups.google.com/forum/#!forum/cobra-toolbox

In order to honor your contribution, we will evaluate your contributions, since the publication of the v2 protocol June 2017, based on the following weighted criteria as a guideline:

25%: Number of contributed tutorials (.mlx format) / Total number of tutorials

15%: Number of commits / Total number of commits (square root)

15%: Number of submitted & merged PRs / Total number of submitted & merged PRs

15%: Number of support messages on forum & issues / Total number of support messages on forum & issues

15%: Number of lines added / Total number of lines added

15%: Number of lines removed / Total number of lines removed

With a significant contribution based on the weighting above, your authorship on the publication will be assured. Principal investigators of the most significantly contributing individuals will also be added to the senior authors list, unless they elect otherwise. The order of authors on the publication will be determined based on the contribution guideline. The basis for this decision will be transparently disseminated via www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. Please note that the last

COBRA Toolbox protocol paper (doi:10.1038/nprot.2011.308) has been cited in excess of 700 times, illustrating the breadth of our community.

Please also note the citation guideline for users of The COBRA Toolbox, where we ask people to cite the original paper that first reported a new algorithm as well as the appropriate COBRA Toolbox paper, so that we ensure creation and dissemination are both credited.

We are looking forward to your contributions!

Regards,

Dr. Ronan M.T. Fleming,

Lead COBRA Toolbox developer (since December 2015).

================

On 4 May 2017 at 17:10, acalapez notifications@github.com wrote:

Hi

Thank you so much for your reply. I am familiar with git. I have not made any pull requests because I am not aware of your policies regarding (outside) contributions and didn't want to mess with your work.

I did circumvent the issue by writing an "updateCobraToolboxFix.m" outside the git repository folder (but still on matlab path) and using it to update. There were a few update issues in the development branch but since I'm was trying to make a model work with the code in master I didn't recorded them (I can check that during the weekend if you wish).

If I may bother you a little more, I am trying to optimize a yeast reaction model written in SMBL that was delivered to me "as is". I am getting a number of warnings concerning an entry "sgd" that supposedly reports to some data in the EMBL database. I haven't been able to check exactly what is it but apparently some reactions are left out. I haven't reported this because I am not sure if it qualifies as a bug. Probably it qualifies as a "unsupported" entry. Are you aware of anything like this and if so, how to solve it? (e.g. alternative SMBL readers)

Thank you in advance...

Looking forward for the new updates

AC

On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt < notifications@github.com

wrote:

Thanks @acalapez https://github.com/acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes

and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools <https://github.com/opencobra/ MATLAB.devTools .

If you however want to update (⚠️ your changes will be lost), you can do the following from the terminal:

$ git stash $ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299100860 <29%2091%2000%20860>>, or mute the thread https://github.com/notifications/unsubscribe- auth/AbDx2-OW84-Vgjd- hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299214632 <29%2092%2014%20632>>, or mute the thread https://github.com/notifications/unsubscribe- auth/ACDCOmxnUN1hx-WFI- Y7zFa9Ot2mGf0Pks5r2epmgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <+352%20621%20175%20112> <621%20175%20112> <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuec omment-299231118, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-NYr kJOnA2YUPjHmSN3k12MIZ4cks5r2fbJgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299246938, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOhOKUSqww8rGcR- VRyuVHUmpzClHks5r2gRegaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <+352%20621%20175%20112> <621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299260899, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx28kzWR7Suik9prbN2Tc_0MMG4yDpks5r2hCRgaJpZM4NQH0r .

rmtfleming commented 7 years ago

Hi, I meant, who is the person behind acalapez? Regards, Ronan

On 4 May 2017 at 20:33, acalapez notifications@github.com wrote:

Hi

Thanks. Will do.

https://github.com/acalapez is my (newly created) personal account at github.

Regards

AC

On Thu, May 4, 2017 at 6:53 PM, Ronan M.T. Fleming < notifications@github.com

wrote:

https://github.com/acalapez is who?

On 4 May 2017 at 19:49, Ronan M.T. Fleming ronan.mt.fleming@gmail.com wrote:

Hi AC,

try http://sbml.org/Facilities/Validator/ this with your xml file.

Regards,

Ronan

On 4 May 2017 at 19:01, acalapez notifications@github.com wrote:

Hi Ronan

I'm working primarily with ADMM based optimization. This is a kind of side-project someone asked me to look into. Still, I'd be happy to get involved (at least as much as I could fit into my schedule). In the weekend I'll take a look at the link you just sent and see how I may contribute.

Regarding the SMBL issue, I'll try to figure it out. Indeed, I'm suspecting some kind of misspecification (or lack of experience with CTB on my side), and for this reason I find it premature to post it as an issue. I can still send the xml and the matlab (2016b) output if you tell me where (or to whom) to, if I find no way to circumvent the issue.

I'll keep you posted (or someone else, if you prefer) as to my availability to contribute.

Best regards

AC

On Thu, May 4, 2017 at 5:03 PM, Ronan M.T. Fleming < notifications@github.com

wrote:

Hi AC,

below is a recent request for contributions.

A function very similar to your update cobra toolbox function is also in the devel branch at the moment and undergoing testing. We want to make it as easy as possible for people to contribute and get others contributions.

As for the yeast model io issue, I am not sure. If you are using all of the latest cobra toolbox functions then it could be a bug in our code, or the code for SBML import or it could be due to misspecification of the .xml file somehow. We put a lot of effort into updating the io functionality with Sarah. If you post here the detailed warnings/errors then we can look at them, but we are not responsible if it is a misspecification of the .xml file.

Regards,

Ronan

==================

Dear user and developer of The COBRA Toolbox,

over the last years, the developer community has assembled a comprehensive suite of COBRA methods and algorithms, tutorials, and tests. As the code base grew larger in size, the code complexity inevitably increased. In order to redress this situation, we launched a significant effort in October 2016 to improve the user friendliness and accessibility through easy-to-follow tutorials and documentation. We set up a continuous integration (CI) server that is testing automatically every change in the code in order to ensure high quality, stable code, and ultimately, guarantee reproducibility of results.

The developer community has been very active over the last months. Nonetheless, The COBRA Toolbox cannot be turned into a comprehensive professional code base for constraint-based reconstruction and analysis without the contributions of the community. That is the reason why we reach out to you - help your community grow!

We aim to submit a publication to Nature Protocols by the end of June 2017 that will highlight the user friendliness, new features, and improved quality of The COBRA Toolbox. In order to overachieve on this goal, we need your support with code contributions, elaborating tutorials, writing tests for existing code, and feedback.

Please note that while MATLAB is used as the main language within The COBRA Toolbox, we already have selectively interfaced to some algorithms in other languages, including perl, python, C, julia and many binaries. We welcome the computational language agnostic, open source development of all forms of COBRA code and welcome support to integrate with complementary tools, including within the broader https://opencobra.github.io/community effort.

You will find instructions on how to contribute on www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. As The COBRA Toolbox is tracked using the git versioning system, you might feel overwhelmed with submitting your contribution as a pull request (PR). The newly released MATLAB.devTools (www.github.com/opencobra/ http://www.github.com/opencobra/MATLAB.devTools) that we developed specifically for this project, allows you to easily submit your contribution from within MATLAB. We look forward to hearing from you and reading your pull request! If you need help, please feel free to post in our forum on www.groups.google.com/forum/#!forum/cobra-toolbox

In order to honor your contribution, we will evaluate your contributions, since the publication of the v2 protocol June 2017, based on the following weighted criteria as a guideline:

25%: Number of contributed tutorials (.mlx format) / Total number of tutorials

15%: Number of commits / Total number of commits (square root)

15%: Number of submitted & merged PRs / Total number of submitted & merged PRs

15%: Number of support messages on forum & issues / Total number of support messages on forum & issues

15%: Number of lines added / Total number of lines added

15%: Number of lines removed / Total number of lines removed

With a significant contribution based on the weighting above, your authorship on the publication will be assured. Principal investigators of the most significantly contributing individuals will also be added to the senior authors list, unless they elect otherwise. The order of authors on the publication will be determined based on the contribution guideline. The basis for this decision will be transparently disseminated via www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. Please note that the last

COBRA Toolbox protocol paper (doi:10.1038/nprot.2011.308) has been cited in excess of 700 times, illustrating the breadth of our community.

Please also note the citation guideline for users of The COBRA Toolbox, where we ask people to cite the original paper that first reported a new algorithm as well as the appropriate COBRA Toolbox paper, so that we ensure creation and dissemination are both credited.

We are looking forward to your contributions!

Regards,

Dr. Ronan M.T. Fleming,

Lead COBRA Toolbox developer (since December 2015).

================

On 4 May 2017 at 17:10, acalapez notifications@github.com wrote:

Hi

Thank you so much for your reply. I am familiar with git. I have not made any pull requests because I am not aware of your policies regarding (outside) contributions and didn't want to mess with your work.

I did circumvent the issue by writing an "updateCobraToolboxFix.m" outside the git repository folder (but still on matlab path) and using it to update. There were a few update issues in the development branch but since I'm was trying to make a model work with the code in master I didn't recorded them (I can check that during the weekend if you wish).

If I may bother you a little more, I am trying to optimize a yeast reaction model written in SMBL that was delivered to me "as is". I am getting a number of warnings concerning an entry "sgd" that supposedly reports to some data in the EMBL database. I haven't been able to check exactly what is it but apparently some reactions are left out. I haven't reported this because I am not sure if it qualifies as a bug. Probably it qualifies as a "unsupported" entry. Are you aware of anything like this and if so, how to solve it? (e.g. alternative SMBL readers)

Thank you in advance...

Looking forward for the new updates

AC

On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt < notifications@github.com

wrote:

Thanks @acalapez https://github.com/acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes

and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools <https://github.com/opencobra/ MATLAB.devTools .

If you however want to update (⚠️ your changes will be lost), you can do the following from the terminal:

$ git stash $ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299100860 <29%2091%2000%20860> <29%2091%2000%20860>>, or mute the thread https://github.com/notifications/unsubscribe- auth/AbDx2-OW84-Vgjd- hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299214632 <29%2092%2014%20632> <29%2092%2014%20632>>, or mute the thread https://github.com/notifications/unsubscribe- auth/ACDCOmxnUN1hx-WFI- Y7zFa9Ot2mGf0Pks5r2epmgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <621%20175%20112> <+352%20621%20175%20112> <621%20175%20112> <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412#issuec omment-299231118 <29%2092%2031%20118>>, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-NYr kJOnA2YUPjHmSN3k12MIZ4cks5r2fbJgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299246938 <29%2092%2046%20938>>, or mute the thread https://github.com/notifications/unsubscribe- auth/ACDCOhOKUSqww8rGcR- VRyuVHUmpzClHks5r2gRegaJpZM4NQH0r

.

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <621%20175%20112> <+352%20621%20175%20112> <621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <621%20175%20112> <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299260899, or mute the thread https://github.com/notifications/unsubscribe- auth/AbDx28kzWR7Suik9prbN2Tc_0MMG4yDpks5r2hCRgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299271356, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDCOvRKg1Dp6RtH2eovllW2D6sog2qAks5r2hnkgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

acalapez commented 7 years ago

Hi

Sorry, I thought you were asking about the account...

My name is Alexandre Calapez.

I am a presently a researcher at the Evolutionary Systems and Biomedical Engineering Lab (https://wiki.laseeb.org/) which is a group in the Institute for Systems and Robotics ( http://welcome.isr.tecnico.ulisboa.pt/), Instituto Superior Técnico ( https://tecnico.ulisboa.pt/en/), University of Lisbon, working under a research grant from the Portuguese Science and Technology Foundation and trying to finish the PhD program in Electrical Engineering at Lisbon University.

Lately, I've been dealing mostly with total-variation regularized inverse problems applied to microscopy and (as I said before) ADMM-based optimization. In the past I had some experience with the characterization and modelling of dynamical systems applied to molecular biology and the processing of biomedical signals (mostly EEG). For some time I was a (C++) programmer at a small Portuguese computer games company, developing an engine for realistic fluid dynamics simulation using GPUs.

I do have extensive experience with Matlab (including mex) and C++.

I'm not sure what you wish to know but I hope this covers it.

Best regards

AC

On Thu, May 4, 2017 at 7:56 PM, Ronan M.T. Fleming <notifications@github.com

wrote:

Hi, I meant, who is the person behind acalapez? Regards, Ronan

On 4 May 2017 at 20:33, acalapez notifications@github.com wrote:

Hi

Thanks. Will do.

https://github.com/acalapez is my (newly created) personal account at github.

Regards

AC

On Thu, May 4, 2017 at 6:53 PM, Ronan M.T. Fleming < notifications@github.com

wrote:

https://github.com/acalapez is who?

On 4 May 2017 at 19:49, Ronan M.T. Fleming <ronan.mt.fleming@gmail.com

wrote:

Hi AC,

try http://sbml.org/Facilities/Validator/ this with your xml file.

Regards,

Ronan

On 4 May 2017 at 19:01, acalapez notifications@github.com wrote:

Hi Ronan

I'm working primarily with ADMM based optimization. This is a kind of side-project someone asked me to look into. Still, I'd be happy to get involved (at least as much as I could fit into my schedule). In the weekend I'll take a look at the link you just sent and see how I may contribute.

Regarding the SMBL issue, I'll try to figure it out. Indeed, I'm suspecting some kind of misspecification (or lack of experience with CTB on my side), and for this reason I find it premature to post it as an issue. I can still send the xml and the matlab (2016b) output if you tell me where (or to whom) to, if I find no way to circumvent the issue.

I'll keep you posted (or someone else, if you prefer) as to my availability to contribute.

Best regards

AC

On Thu, May 4, 2017 at 5:03 PM, Ronan M.T. Fleming < notifications@github.com

wrote:

Hi AC,

below is a recent request for contributions.

A function very similar to your update cobra toolbox function is also in the devel branch at the moment and undergoing testing. We want to make it as easy as possible for people to contribute and get others contributions.

As for the yeast model io issue, I am not sure. If you are using all of the latest cobra toolbox functions then it could be a bug in our code, or the code for SBML import or it could be due to misspecification of the .xml file somehow. We put a lot of effort into updating the io functionality with Sarah. If you post here the detailed warnings/errors then we can look at them, but we are not responsible if it is a misspecification of the .xml file.

Regards,

Ronan

==================

Dear user and developer of The COBRA Toolbox,

over the last years, the developer community has assembled a comprehensive suite of COBRA methods and algorithms, tutorials, and tests. As the code base grew larger in size, the code complexity inevitably increased. In order to redress this situation, we launched a significant effort in October 2016 to improve the user friendliness and accessibility through easy-to-follow tutorials and documentation. We set up a continuous integration (CI) server that is testing automatically every change in the code in order to ensure high quality, stable code, and ultimately, guarantee reproducibility of results.

The developer community has been very active over the last months. Nonetheless, The COBRA Toolbox cannot be turned into a comprehensive professional code base for constraint-based reconstruction and analysis without the contributions of the community. That is the reason why we reach out to you - help your community grow!

We aim to submit a publication to Nature Protocols by the end of June 2017 that will highlight the user friendliness, new features, and improved quality of The COBRA Toolbox. In order to overachieve on this goal, we need your support with code contributions, elaborating tutorials, writing tests for existing code, and feedback.

Please note that while MATLAB is used as the main language within The COBRA Toolbox, we already have selectively interfaced to some algorithms in other languages, including perl, python, C, julia and many binaries. We welcome the computational language agnostic, open source development of all forms of COBRA code and welcome support to integrate with complementary tools, including within the broader https://opencobra.github.io/ community effort.

You will find instructions on how to contribute on www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. As The COBRA Toolbox is tracked using the git versioning system, you might feel overwhelmed with submitting your contribution as a pull request (PR). The newly released MATLAB.devTools (www.github.com/opencobra/ http://www.github.com/opencobra/MATLAB.devTools) that we developed specifically for this project, allows you to easily submit your contribution from within MATLAB. We look forward to hearing from you and reading your pull request! If you need help, please feel free to post in our forum on www.groups.google.com/forum/#!forum/cobra-toolbox

In order to honor your contribution, we will evaluate your contributions, since the publication of the v2 protocol June 2017, based on the following weighted criteria as a guideline:

25%: Number of contributed tutorials (.mlx format) / Total number of tutorials

15%: Number of commits / Total number of commits (square root)

15%: Number of submitted & merged PRs / Total number of submitted & merged PRs

15%: Number of support messages on forum & issues / Total number of support messages on forum & issues

15%: Number of lines added / Total number of lines added

15%: Number of lines removed / Total number of lines removed

With a significant contribution based on the weighting above, your authorship on the publication will be assured. Principal investigators of the most significantly contributing individuals will also be added to the senior authors list, unless they elect otherwise. The order of authors on the publication will be determined based on the contribution guideline. The basis for this decision will be transparently disseminated via www.github.com/opencobra/ http://www.github.com/opencobra/cobratoolbox. Please note that the last

COBRA Toolbox protocol paper (doi:10.1038/nprot.2011.308) has been cited in excess of 700 times, illustrating the breadth of our community.

Please also note the citation guideline for users of The COBRA Toolbox, where we ask people to cite the original paper that first reported a new algorithm as well as the appropriate COBRA Toolbox paper, so that we ensure creation and dissemination are both credited.

We are looking forward to your contributions!

Regards,

Dr. Ronan M.T. Fleming,

Lead COBRA Toolbox developer (since December 2015).

================

On 4 May 2017 at 17:10, acalapez notifications@github.com wrote:

Hi

Thank you so much for your reply. I am familiar with git. I have not made any pull requests because I am not aware of your policies regarding (outside) contributions and didn't want to mess with your work.

I did circumvent the issue by writing an "updateCobraToolboxFix.m" outside the git repository folder (but still on matlab path) and using it to update. There were a few update issues in the development branch but since I'm was trying to make a model work with the code in master I didn't recorded them (I can check that during the weekend if you wish).

If I may bother you a little more, I am trying to optimize a yeast reaction model written in SMBL that was delivered to me "as is". I am getting a number of warnings concerning an entry "sgd" that supposedly reports to some data in the EMBL database. I haven't been able to check exactly what is it but apparently some reactions are left out. I haven't reported this because I am not sure if it qualifies as a bug. Probably it qualifies as a "unsupported" entry. Are you aware of anything like this and if so, how to solve it? (e.g. alternative SMBL readers)

Thank you in advance...

Looking forward for the new updates

AC

On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt < notifications@github.com

wrote:

Thanks @acalapez https://github.com/acalapez for reporting this. The issue with == has already been fixed on the develop branch and will be released soon with other fixes.

The reason the CBT cannot update is because you have made changes

and the updateCobraToolbox function does not overwrite these. You can check which files have been changed using (from the Terminal):

$ git status # check the status and lists your files

and, in more detail:

$ git status # check the status and lists your files

If you want to contribute, you need to make changes to your fork and submit a Pull Request (PR). If you are not too familiar with git, you can use the MATLAB.devTools <https://github.com/opencobra/ MATLAB.devTools .

If you however want to update (⚠️ your changes will be lost), you can do the following from the terminal:

$ git stash $ git clean -d -f # changes will be lost!

I will close the issue now, as the reported bug has already been fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299100860 <29%2091%2000%20860> <29%2091%2000%20860>>, or mute the thread https://github.com/notifications/unsubscribe- auth/AbDx2-OW84-Vgjd- hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299214632 <29%2092%2014%20632> <29%2092%2014%20632>>,

or mute the thread https://github.com/notifications/unsubscribe- auth/ACDCOmxnUN1hx-WFI- Y7zFa9Ot2mGf0Pks5r2epmgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <+352%20621%20175%20112> <621%20175%20112> <+352%20621%20175%20112> <621%20175%20112> <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412#issuec omment-299231118 <29%2092%2031%20118>>, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx2-NYr kJOnA2YUPjHmSN3k12MIZ4cks5r2fbJgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299246938 <29%2092%2046%20938>>, or mute the thread <https://github.com/notifications/unsubscribe- auth/ACDCOhOKUSqww8rGcR-

VRyuVHUmpzClHks5r2gRegaJpZM4NQH0r>

.

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <+352%20621%20175%20112> <621%20175%20112> <+352%20621%20175%20112> <621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <+352%20621%20175%20112> <621%20175%20112> <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299260899, or mute the thread https://github.com/notifications/unsubscribe- auth/AbDx28kzWR7Suik9prbN2Tc_0MMG4yDpks5r2hCRgaJpZM4NQH0r .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412# issuecomment-299271356, or mute the thread https://github.com/notifications/unsubscribe-auth/ ACDCOvRKg1Dp6RtH2eovllW2D6sog2qAks5r2hnkgaJpZM4NQH0r .

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Senior research associate (EN) == Chercheur (FR), Principal investigator, Systems Biochemistry Group, wwwen.uni.lu/lcsb/research/systems_biochemistry Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux. & National Centre of Excellence in Research on Parkinson’s disease www.parkinson.lu & Adjunct Assistant Professor, Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden. http://analyticalbiosciences.leidenuniv.nl

Mobile: +352 621 175 112 <+352%20621%20175%20112> Office: +352 466 644 5528 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299277496, or mute the thread https://github.com/notifications/unsubscribe-auth/AbDx275G1Qb6IRFxw1MCzQ1ckFvKACHEks5r2h96gaJpZM4NQH0r .