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ModelSEED UI (beta)
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Custom media compositions for peptides #49

Closed anna0101 closed 5 years ago

anna0101 commented 8 years ago

Hi,

I am trying to create new media compositions that include dipeptides and tripeptides but can't find any of these compounds within Model Seed to add to the media.

Would you be able to help us with this please? Is there a way to add new dipeptides and tripeptides compounds with the corresponding ID, Formula, deltaG, detalGerr and charge for each peptide?

Many thanks

Anna

chian commented 8 years ago

Hi Anna,

I will let someone else who knows better provide the details, but the biochemistry file is available in the github repository. You should be able to and feel free to take out a branch and add any missing metabolites and reactions you need for your model. After that we should be able to merge the changes if all went well with the changes.

Or if you are running independently, you should be able to launch ModelSeed with your biochemistry file.

Hope that helps!

Best, Nick

Sent from my iPhone

On Aug 3, 2016, at 5:29 PM, anna0101 notifications@github.com wrote:

Hi,

I am trying to create new media compositions that include dipeptides and tripeptides but can't find any of these compounds within Model Seed to add to the media.

Would you be able to help us with this please? Is there a way to add new dipeptides and tripeptides compounds with the corresponding ID, Formula, deltaG, detalGerr and charge for each peptide?

Many thanks

Anna

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

anna0101 commented 8 years ago

Hi Nick,

Thanks for your email.

Would you be able to send me the biochemistry file please? I can't seem to find it in the repository.

Many thanks

Anna

From: chian notifications@github.com Sent: 03 August 2016 23:39 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Author Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Hi Anna,

I will let someone else who knows better provide the details, but the biochemistry file is available in the github repository. You should be able to and feel free to take out a branch and add any missing metabolites and reactions you need for your model. After that we should be able to merge the changes if all went well with the changes.

Or if you are running independently, you should be able to launch ModelSeed with your biochemistry file.

Hope that helps!

Best, Nick

Sent from my iPhone

On Aug 3, 2016, at 5:29 PM, anna0101 notifications@github.com wrote:

Hi,

I am trying to create new media compositions that include dipeptides and tripeptides but can't find any of these compounds within Model Seed to add to the media.

Would you be able to help us with this please? Is there a way to add new dipeptides and tripeptides compounds with the corresponding ID, Formula, deltaG, detalGerr and charge for each peptide?

Many thanks

Anna

You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

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jplfaria commented 8 years ago

Hi Anna,

This is our biochemistry repo: https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry

You can checkout the repo add your cpds and then submit a PR to the repo

anna0101 commented 8 years ago

Hi Nick,

I previously had annotated genomes imported from RAST into the "genome" and "mine" folder within Model Seed but these have suddenly disappeared. I can still see the annotated genomes in RAST and in the "all my files" folder but i can't see them in the "mine" genomes folder.

Please advise,

Many thanks.

Anna

From: chian notifications@github.com Sent: 03 August 2016 23:39 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Author Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Hi Anna,

I will let someone else who knows better provide the details, but the biochemistry file is available in the github repository. You should be able to and feel free to take out a branch and add any missing metabolites and reactions you need for your model. After that we should be able to merge the changes if all went well with the changes.

Or if you are running independently, you should be able to launch ModelSeed with your biochemistry file.

Hope that helps!

Best, Nick

Sent from my iPhone

On Aug 3, 2016, at 5:29 PM, anna0101 notifications@github.com wrote:

Hi,

I am trying to create new media compositions that include dipeptides and tripeptides but can't find any of these compounds within Model Seed to add to the media.

Would you be able to help us with this please? Is there a way to add new dipeptides and tripeptides compounds with the corresponding ID, Formula, deltaG, detalGerr and charge for each peptide?

Many thanks

Anna

You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

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chian commented 8 years ago

Anna,

This is going to have to be a @chrishenry question.

Best, Nick

Sent from my iPhone

On Aug 4, 2016, at 7:28 AM, anna0101 notifications@github.com wrote:

Hi Nick,

I previously had annotated genomes imported from RAST into the "genome" and "mine" folder within Model Seed but these have suddenly disappeared. I can still see the annotated genomes in RAST and in the "all my files" folder but i can't see them in the "mine" genomes folder.

Please advise,

Many thanks.

Anna

From: chian notifications@github.com Sent: 03 August 2016 23:39 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Author Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Hi Anna,

I will let someone else who knows better provide the details, but the biochemistry file is available in the github repository. You should be able to and feel free to take out a branch and add any missing metabolites and reactions you need for your model. After that we should be able to merge the changes if all went well with the changes.

Or if you are running independently, you should be able to launch ModelSeed with your biochemistry file.

Hope that helps!

Best, Nick

Sent from my iPhone

On Aug 3, 2016, at 5:29 PM, anna0101 notifications@github.com wrote:

Hi,

I am trying to create new media compositions that include dipeptides and tripeptides but can't find any of these compounds within Model Seed to add to the media.

Would you be able to help us with this please? Is there a way to add new dipeptides and tripeptides compounds with the corresponding ID, Formula, deltaG, detalGerr and charge for each peptide?

Many thanks

Anna

You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ModelSEED/ModelSEED-UI/issues/49#issuecomment-237397325, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT3H1GI0IFiH8iD9WFpuS3xY8gsiNl3iks5qcRi2gaJpZM4JcKby. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

anna0101 commented 8 years ago

Hi Nick,

Sorry to keep emailing you. Do you have the email address for @chrishenry?

Many thanks

Anna

Get Outlook for iOShttps://aka.ms/o0ukef

From: chian notifications@github.com<mailto:notifications@github.com> Sent: Thursday, August 4, 2016 4:45 pm Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49) To: ModelSEED/ModelSEED-UI modelseed-ui@noreply.github.com<mailto:modelseed-ui@noreply.github.com> Cc: Annapaula Correia (MED) a.correia@uea.ac.uk<mailto:a.correia@uea.ac.uk>, Author author@noreply.github.com<mailto:author@noreply.github.com>

Anna,

This is going to have to be a @chrishenry question.

Best, Nick

Sent from my iPhone

On Aug 4, 2016, at 7:28 AM, anna0101 notifications@github.com<mailto:notifications@github.com> wrote:

Hi Nick,

I previously had annotated genomes imported from RAST into the "genome" and "mine" folder within Model Seed but these have suddenly disappeared. I can still see the annotated genomes in RAST and in the "all my files" folder but i can't see them in the "mine" genomes folder.

Please advise,

Many thanks.

Anna

From: chian notifications@github.com<mailto:notifications@github.com> Sent: 03 August 2016 23:39 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Author Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Hi Anna,

I will let someone else who knows better provide the details, but the biochemistry file is available in the github repository. You should be able to and feel free to take out a branch and add any missing metabolites and reactions you need for your model. After that we should be able to merge the changes if all went well with the changes.

Or if you are running independently, you should be able to launch ModelSeed with your biochemistry file.

Hope that helps!

Best, Nick

Sent from my iPhone

On Aug 3, 2016, at 5:29 PM, anna0101 notifications@github.com<mailto:notifications@github.com> wrote:

Hi,

I am trying to create new media compositions that include dipeptides and tripeptides but can't find any of these compounds within Model Seed to add to the media.

Would you be able to help us with this please? Is there a way to add new dipeptides and tripeptides compounds with the corresponding ID, Formula, deltaG, detalGerr and charge for each peptide?

Many thanks

Anna

You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

You are receiving this because you authored the thread.

Reply to this email directly, view it on GitHubhttps://github.com/ModelSEED/ModelSEED-UI/issues/49#issuecomment-237397325, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT3H1GI0IFiH8iD9WFpuS3xY8gsiNl3iks5qcRi2gaJpZM4JcKby.

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chian commented 8 years ago

Anna,

Not a problem. The communications are great. I like seeing the broader involvement we've gotten recently!

I've cc'd Chris Henry. Feel free to email again if you don't get a reply.

Best, Nick

Sent from my iPhone

On Aug 4, 2016, at 12:42 PM, anna0101 notifications@github.com wrote:

Hi Nick,

Sorry to keep emailing you. Do you have the email address for @chrishenry?

Many thanks

Anna

Get Outlook for iOShttps://aka.ms/o0ukef

From: chian notifications@github.com<mailto:notifications@github.com> Sent: Thursday, August 4, 2016 4:45 pm Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49) To: ModelSEED/ModelSEED-UI modelseed-ui@noreply.github.com<mailto:modelseed-ui@noreply.github.com> Cc: Annapaula Correia (MED) a.correia@uea.ac.uk<mailto:a.correia@uea.ac.uk>, Author author@noreply.github.com<mailto:author@noreply.github.com>

Anna,

This is going to have to be a @chrishenry question.

Best, Nick

Sent from my iPhone

On Aug 4, 2016, at 7:28 AM, anna0101 notifications@github.com<mailto:notifications@github.com> wrote:

Hi Nick,

I previously had annotated genomes imported from RAST into the "genome" and "mine" folder within Model Seed but these have suddenly disappeared. I can still see the annotated genomes in RAST and in the "all my files" folder but i can't see them in the "mine" genomes folder.

Please advise,

Many thanks.

Anna

From: chian notifications@github.com<mailto:notifications@github.com> Sent: 03 August 2016 23:39 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Author Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Hi Anna,

I will let someone else who knows better provide the details, but the biochemistry file is available in the github repository. You should be able to and feel free to take out a branch and add any missing metabolites and reactions you need for your model. After that we should be able to merge the changes if all went well with the changes.

Or if you are running independently, you should be able to launch ModelSeed with your biochemistry file.

Hope that helps!

Best, Nick

Sent from my iPhone

On Aug 3, 2016, at 5:29 PM, anna0101 notifications@github.com<mailto:notifications@github.com> wrote:

Hi,

I am trying to create new media compositions that include dipeptides and tripeptides but can't find any of these compounds within Model Seed to add to the media.

Would you be able to help us with this please? Is there a way to add new dipeptides and tripeptides compounds with the corresponding ID, Formula, deltaG, detalGerr and charge for each peptide?

Many thanks

Anna

You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

You are receiving this because you authored the thread.

Reply to this email directly, view it on GitHubhttps://github.com/ModelSEED/ModelSEED-UI/issues/49#issuecomment-237397325, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT3H1GI0IFiH8iD9WFpuS3xY8gsiNl3iks5qcRi2gaJpZM4JcKby.

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chrishenry commented 8 years ago

Hi @chian. As I am the wrong Chris Henry, I don't think I'll be able to help with your annotated genome files.

However, I would recommend minifying and concat'ing your JS, as it looks like you have quite a large payload.

Best of luck!

nconrad commented 8 years ago

Hi @anna0101, the rast-annotated genomes list issue (under "mine") was fixed earlier today. There was a power outage causing the server to go down for some time.

@chrishenry, I am minifying and concat'ing JS with https://github.com/ModelSEED/ModelSEED-UI#build for the time being. Sorry for the mixup.

anna0101 commented 8 years ago

Hello,

I am trying to add new compounds (dipeptides and tripeptides) to the model seed database so I can perform metabolic reconstructions. Do I just need to modify the compounds.master.tsv file or do I also need to modify the compartments.master.tsv and reactions.master.tsv files as well? I ask as I cant seem to find any information on dipeptides and tripeptides with regards to reaction pathways (rxns) and compartment data.

Many thanks

Anna

From: jplfaria notifications@github.com Sent: 04 August 2016 00:01 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Author Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Hi Anna,

This is our biochemistry repo: https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry

[https://avatars1.githubusercontent.com/u/1045967?v=3&s=400]https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry

ModelSEEDDatabase/Biochemistry at master · ModelSEED ...https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry github.com ModelSEEDDatabase - This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach

You can checkout the repo add your cpds and then submit a pull request.

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ModelSEED/ModelSEED-UI/issues/49#issuecomment-237401690, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT3H1L0Mj-9-YAHx9oFja0Ds7kq8gheSks5qcR3egaJpZM4JcKby.

chian commented 8 years ago

Anna,

You'll have to modify all of those to get the right reactions in the right places. Otherwise the compounds will have no attachment to any other reaction/compounds in the model.

Best, Nick

Sent from my iPhone

On Aug 8, 2016, at 9:15 AM, anna0101 notifications@github.com wrote:

Hello,

I am trying to add new compounds (dipeptides and tripeptides) to the model seed database so I can perform metabolic reconstructions. Do I just need to modify the compounds.master.tsv file or do I also need to modify the compartments.master.tsv and reactions.master.tsv files as well? I ask as I cant seem to find any information on dipeptides and tripeptides with regards to reaction pathways (rxns) and compartment data.

Many thanks

Anna

From: jplfaria notifications@github.com Sent: 04 August 2016 00:01 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Author Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Hi Anna,

This is our biochemistry repo: https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry

[https://avatars1.githubusercontent.com/u/1045967?v=3&s=400]https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry

ModelSEEDDatabase/Biochemistry at master · ModelSEED ...https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry github.com ModelSEEDDatabase - This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach

You can checkout the repo add your cpds and then submit a pull request.

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ModelSEED/ModelSEED-UI/issues/49#issuecomment-237401690, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT3H1L0Mj-9-YAHx9oFja0Ds7kq8gheSks5qcR3egaJpZM4JcKby. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

anna0101 commented 8 years ago

Thanks Nick,

I'll start modifying the files. I've tried adding some new media to the "my media" folder but it doesn't seem to be working. I'm guessing the server isn't working well right now?

Anna

From: chian notifications@github.com Sent: 08 August 2016 20:23 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Mention Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Anna,

You'll have to modify all of those to get the right reactions in the right places. Otherwise the compounds will have no attachment to any other reaction/compounds in the model.

Best, Nick

Sent from my iPhone

On Aug 8, 2016, at 9:15 AM, anna0101 notifications@github.com wrote:

Hello,

I am trying to add new compounds (dipeptides and tripeptides) to the model seed database so I can perform metabolic reconstructions. Do I just need to modify the compounds.master.tsv file or do I also need to modify the compartments.master.tsv and reactions.master.tsv files as well? I ask as I cant seem to find any information on dipeptides and tripeptides with regards to reaction pathways (rxns) and compartment data.

Many thanks

Anna

From: jplfaria notifications@github.com Sent: 04 August 2016 00:01 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Author Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Hi Anna,

This is our biochemistry repo: https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry

[https://avatars1.githubusercontent.com/u/1045967?v=3&s=400]https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry

ModelSEEDDatabase/Biochemistry at master · ModelSEED ...https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry github.com ModelSEEDDatabase - This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach

You can checkout the repo add your cpds and then submit a pull request.

You are receiving this because you authored the thread.

Reply to this email directly, view it on GitHubhttps://github.com/ModelSEED/ModelSEED-UI/issues/49#issuecomment-237401690, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT3H1L0Mj-9-YAHx9oFja0Ds7kq8gheSks5qcR3egaJpZM4JcKby.

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

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mmundy42 commented 8 years ago

Anna,

Here are some more details for you. You'll need to add new compounds and reactions in https://github.com/ModelSEED/ModelSEEDDatabase. The first step is update the master biochemistry files. Look in https://github.com/ModelSEED/ModelSEEDDatabase/blob/master/Biochemistry/README.md for information on the format of the files. The reaction and compound IDs need to be unique.

The second step is to update the templates that are used for reconstructing models of your organisms. Look in https://github.com/ModelSEED/ModelSEEDDatabase/blob/master/Templates/README.md for information on the format of the files and directions for building a template.

If the README files don't make sense, post an issue in the ModelSEEDDatabase repo and I can try to clarify.

anna0101 commented 8 years ago

Thanks Mike,

I am trying to perform reconstructions with custom modified media but it keeps failing. I have substituted glucose with succinate. Attached is an example of a file I am working with. Please advise

Thanks

Anna

From: Mike Mundy notifications@github.com Sent: 09 August 2016 16:56 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Mention Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Anna,

Here are some more details for you. You'll need to add new compounds and reactions in https://github.com/ModelSEED/ModelSEEDDatabase. The first step is update the master biochemistry files. Look in https://github.com/ModelSEED/ModelSEEDDatabase/blob/master/Biochemistry/README.md for information on the format of the files. The reaction and compound IDs need to be unique.

[https://avatars1.githubusercontent.com/u/1045967?v=3&s=400]https://github.com/ModelSEED/ModelSEEDDatabase

GitHub - ModelSEED/ModelSEEDDatabase: This repository ...https://github.com/ModelSEED/ModelSEEDDatabase github.com ModelSEEDDatabase - This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach

The second step is to update the templates that are used for reconstructing models of your organisms. Look in https://github.com/ModelSEED/ModelSEEDDatabase/blob/master/Templates/README.md for information on the format of the files and directions for building a template.

If the README files don't make sense, post an issue in the ModelSEEDDatabase repo and I can try to clarify.

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ModelSEED/ModelSEED-UI/issues/49#issuecomment-238599382, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT3H1Mb8jM6PR6GHR3NBHbbM6ahzhJpfks5qeKMdgaJpZM4JcKby.

mmundy42 commented 8 years ago

Anna, I don't see a file attached. If it is small, can you paste the contents in a comment?

anna0101 commented 8 years ago

id name concentration minflux maxflux cpd00001 H2O 0.001 -100 100 cpd00007 O2 0.001 -100 100 cpd00011 CO2 0.001 -100 0 cpd00013 NH3 0.001 -100 5 cpd00030 Mn2+ 0.001 -100 100 cpd00034 Zn2+ 0.001 -100 100 cpd00036 Succinate 0.001 -100 100 cpd00048 Sulfate 0.001 -100 5 cpd00058 Cu2+ 0.001 -100 100 cpd00063 Ca2+ 0.001 -100 100 cpd00067 H+ 0.001 -100 100 cpd00099 Cl- 0.001 -100 100 cpd00149 Co2+ 0.001 -100 100 cpd00205 K+ 0.001 -100 100 cpd00254 Mg 0.001 -100 100 cpd00971 Na+ 0.001 -100 100 cpd01665 D-O-Phosphoserine 0.001 -100 5 cpd10515 Fe2+ 0.001 -100 100 cpd10516 fe3 0.001 -100 100

I've substituted Succinate with Glucose in the Phosphate-O-Phospho-D-Serine media. Hope that helps.

From: Mike Mundy notifications@github.com Sent: 09 August 2016 18:51 To: ModelSEED/ModelSEED-UI Cc: Annapaula Correia (MED); Mention Subject: Re: [ModelSEED/ModelSEED-UI] Custom media compositions for peptides (#49)

Anna, I don't see a file attached. If it is small, can you paste the contents in a comment?

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ModelSEED/ModelSEED-UI/issues/49#issuecomment-238634382, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT3H1Da9aUUARWZngivYwHd6I5zeb200ks5qeL4SgaJpZM4JcKby.

samseaver commented 5 years ago

@anna0101 I'm closing without comment. We've made significant changes to the website, so if you encounter any new problems, do let us know.