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    Moritz E. Beber
    @Midnighter
    On that topic, should the respective SBO terms also be double checked?
    Benjamín Sánchez
    @BenjaSanchez
    @Midnighter SBO terms are automatically updated on each model change based on https://github.com/SysBioChalmers/yeast-GEM/blob/master/ComplementaryScripts/missingFields/addSBOterms.m; in particular exchange rxns & transport rxns should always remain correct (even if the name is wrong)
    Moritz E. Beber
    @Midnighter
    Awesome, even better :)
    Benjamín Sánchez
    @BenjaSanchez
    @edkerk btw did you try with the model in devel? model.rxnNames(strcmp(model.rxns,'r_1896')) yields L-homoserine exchange
    Eduard Kerkhoven
    @edkerk
    You're right, it's already fixed there!
    St Elmo
    @stelmo
    Hi, I am busy writing a review paper and I would like to cite the latest version of the model. Is there a citation ya'll could point me to?
    Benjamín Sánchez
    @BenjaSanchez
    @stelmo no paper at the moment, we are working on the manuscript and I can let you know whenever it is submitted/available as preprint. In the meantime:
    Moritz E. Beber
    @Midnighter
    @BenjaSanchez would it be useful to push GitHub releases (tags) of the model to Zenodo where you can then have a DOI for each version of the model?
    Benjamín Sánchez
    @BenjaSanchez
    @Midnighter yes we are considering including that :) will post it here once it is available!
    St Elmo
    @stelmo
    @BenjaSanchez thank you!
    Moritz E. Beber
    @Midnighter
    Would it be helpful if we create an upload script for Zenodo and include it in the .travis.yml provided by memote?
    Moritz E. Beber
    @Midnighter
    Actually, I just checked out the Zenodo GitHub integration and if you activate it they automatically download your releases and provide a DOI for the project. :ok_hand:
    William Scott
    @wtscott31
    @BenjaSanchez I would like to submit an issue and be specific with the updates that need to be made, however, some of the compounds that I would like to add such as ethyl butyrate and ethyl decanoate are not referenced in any database such as KEGG or metacyc. In addition, some compounds e.g. hexyl acetate and ethyl hexanoate are only cited in metacyc , but have no pathway information and very little reaction information regarding their behavior in metabolism and we know these compounds are generated from the degradation of amino acids and fatty acids. Lastly, mostly related to adding fusel alcohols to the model, many of them are produced during the Ehrlich pathway. Is there a way to just add a well-known "complete" pathway such as this to YeastGEM?
    Benjamín Sánchez
    @BenjaSanchez
    @wtscott31 ideally mets/rxns added to the model should count with some level of annotation. If there is nothing in KEGG/metacyc there are other databases more model-driven that could help: model SEED, bigg, metanetx. Perhaps @hongzhonglu can give additional ideas here. In any case, if some of them still remain unmatched, a pmid at least should be provided pointing to the publication that proved the existence of said met/rxn. As long as they are not too many I don't see a problem with adding them, for the sake of network connectivity
    William Scott
    @wtscott31
    @BenjaSanchez Alright! How should I submit this issue/request for the met/rxns to be added? More specifically, is there a preferred format such as listing the pathway, genes, organelles, met/rxns, source, etc.? Additionally, how detailed should I be , for instance, do all of the precursors need to be mentioned? If so, how?
    Benjamín Sánchez
    @BenjaSanchez
    @wtscott31 try to provide all the information that you have and if something is missing we can comment on the issue / guide you for adding the reactions in the best way. Be sure to read the contributing guidelines as well, they have useful information for adding mets/rxns
    Benjamín Sánchez
    @BenjaSanchez
    @stelmo @Midnighter we are now releasing each version in Zenodo, and you can see citation guidelines here: https://github.com/SysBioChalmers/yeast-GEM#citation
    Moritz E. Beber
    @Midnighter
    :tada:
    William Scott
    @wtscott31
    @BenjaSanchez I know I mentioned to you all that I am in the process of creating an open issue for the curation of the model to incorporate Amino Acid Degradation (Ehrlich) pathways and furthermore reactions related to ester production from the higher alcohols produced during AA degradation and fatty acid conversion into the model. However, I am still unsure how to go about that and how extensive should the coverage be since there might be a lot of new reactions (see here a link of all AA degradation pathways https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?object=Amino-Acid-Degradation&detail-level=4&detail-level=3). I am currently using the YeastGEM excel format to add all of the necessary information manually, but is there another way that could be more efficient and expedient. Thanks!
    Benjamín Sánchez
    @BenjaSanchez
    @wtscott31 note that some of those reactions are already included in the model; do you have an estimate on how many would they be in total? I would advice to keep coverage high, but make sure to include everything known of each reaction (including annotation).
    Also, note that currently we do not support changes to the model through yeastGEM.xlsx, as the latter is only in the master branch and thereby always behind the latest changes. You can read the proper way to contribute here and look at an example on how are changes typically included here. Note in particular that all information is added through .tsv tables, which you can construct in excel (just make sure to check later they look ok in a text editor and no weird characters are introduced).
    William Scott
    @wtscott31
    Hi @BenjaSanchez , I am in the process of trying to add Ethyl Ester and other Fatty Acid Ester Biosynthesis reactions to YeastGEM. Furthermore, I am using the example you referred to in the previous message as a template to get started. However, I am not sure which database was used to obtain the ID numbers in the file: Metabolomics_newRxnMatrix.tsv. For example, 2-hydroxyglutarate has MNXR111769. Do you know where those ID numbers originate from? Thanks
    Moritz E. Beber
    @Midnighter
    Hey @wtscott31 that's a MetaNetX identifier http://metanetx.org/ That's a Swiss effort to map different identifiers to each other.
    William Scott
    @wtscott31
    @Midnighter thanks!
    William Scott
    @wtscott31
    @Midnighter It seems the reactions that I would like to add do not contain identifiers in MetaNetX. They are a class of reactions regulated by the EEB1/EHT1 gene for medium-chain fatty acid ethyl ester synthase/esterase. I have only been able to find a reference to the general reaction on this database:https://www.uniprot.org/uniprot/Q02891. Do you know of any other databases that are more detailed?
    Moritz E. Beber
    @Midnighter
    So the reaction that you linked Q02891 originally comes from the RHEA database (it shows 'Source: RHEA' on the Uniprot site). RHEA is fully contained in MetaNetX. So the reaction that you linked has the identifier RHEA:17229 which brings you to https://www.metanetx.org/equa_info/MNXR125910.
    William Scott
    @wtscott31
    @Midnighter Thanks again! I did not know those reactions were contained in MetaNetX. I guess that leads me to another question as to how does one distinguish between the different acetyl esters and/or aliphatic alcohols when referencing this reaction?
    William Scott
    @wtscott31
    For example, I would like to add ethyl hexanoate and ethyl octanoate, and their precursor reactions such as hexanoyl-CoA and octanoyl-CoA to the model, but if those reactions have the same ID wouldn't that confuse accounting/indexing?
    Moritz E. Beber
    @Midnighter
    So if you cannot find a more specific description of your reaction, I suggest the following: Reaction identifiers in the model need to be unique. However, every reaction can have multiple annotations, for example, their Rhea and MetaNetX identifier, which does not need to be unique. What exactly the model internal identifier for a reaction should look like is better answered by someone else here. It should be consistent with other identifiers in the model.
    Benjamín Sánchez
    @BenjaSanchez
    @wtscott31 in general, metabolites and reactions should not have repeated metanetx ids in the model, unless it's the same met/rxn but in a different compartment. But as you point out, some species in metanetx are generic, and imo it's better to have generic information than no information at all. No problem with having then the same metanetx id in those cases, do consider however that you can also add KEGG ids, EC numbers, PMIDs and any other id registered at https://www.ebi.ac.uk/miriam/main/collections to the corresponding COBRA fields
    William Scott
    @wtscott31
    @BenjaSanchez thanks for your reply! I am in the process of submitting my commits and pushing my branch on to Github, however, I am getting a message saying that I do not have access to the repository or that the repository has been archived. I will keep trying though.
    Eduard Kerkhoven
    @edkerk
    @wtscott31 You should fork the repo to your own account and push your commits to the forked repo. Then, you can make a pull request to the devel branch in the original SysBioChalmers repo.
    William Scott
    @wtscott31
    @edkerk Thanks! I will do that and make a pull request today.
    Hoang Dinh
    @hvdinh16
    Hi, I have found some issues with the model yeast 8.3.3 which I think you might be interested to know. They are: (i) r_4592 GPR typo, (ii) Coefficients for cofactor from DOI: 10.1016/j.ymben.2013.11.005 need to be multiplied by the dilution rate 0.1 hr-1. I also wondered why glycolipid is not present in the biomass reaction.
    hongzhonglu
    @hongzhonglu
    @hvdinh16 Thanks for your support. Could you record this as issues in yeast-GEM repo. Later we can solve it.
    feiranl
    @feiranl
    @hvdinh16 Thanks for letting us know. I have noticed that typo, and corrected that in local branch, will merge to the master soon.
    Hoang Dinh
    @hvdinh16
    Thanks, I will just make an issue on biomass coefficients then.
    Hoang Dinh
    @hvdinh16
    My bad on the issue (ii) Coefficients for cofactor from DOI: 10.1016/j.ymben.2013.11.005. I check my unit calculation again and the coefficients do not need to be multiplied by the experimental dilution rate.
    kabilan2818
    @kabilan2818
    how to find the coefficient of ATP in Biomass equation
    hongzhonglu
    @hongzhonglu
    @kabilan2818 you can check this reaction, r_4041 biomass pseudoreaction 55.3 s_0434[c] + 55.3 s_0803[c] + s_1096[c] + s_3717[c] + s_3718[c] + s_3719[c] + s_3720[c] + s_4205[c] + s_4206[c] -> 55.3 s_0394[c] + s_0450[c] + 55.3 s_0794[c] + 55.3 s_1322[c]
    kabilan2818
    @kabilan2818
    Does any one have central carbon metabolic pre drawn model map for plotting the flux
    Simonas Marcišauskas
    @simas232
    @kabilan2818, see the response in RAVEN channel
    William Scott
    @wtscott31
    Hi, I am trying to add missing reactions and pathways that are in YeastGEM using RBioNet. However, I am already experiencing an error when I select Add Reconstruction to Database which gives "structure incorrect: Group gRules is missing from structure of model." How should I approach or fix this problem? Also, is there a more apt method of adding reactions and pathways using CobraToolbox especially if those reactions are produced by genes which are related to a general reaction listed in databases such as "1 CoA + 1 an acetyl ester = 1 acetyl-CoA + 1 an aliphatic alcohol" and I would prefer adding specific metabolites for the esters and alcohols?
    hongzhonglu
    @hongzhonglu
    @wtscott31 You can add the gRules in the model, that is model.gRules = gRules. In yeast GEM, the general reaction should be avoided and it is better to make it in detail.
    William Scott
    @wtscott31
    Thanks @hongzhonglu ! Also, I do not see a .json file, as other models that are in the BIGG database, for yeast-GEM. Perhaps is there one, but maybe I am just not seeing it?
    hongzhonglu
    @hongzhonglu
    @wtscott31 Now we don't have yeast GEM in json format. In the future we can provide it if it is essential.
    William Scott
    @wtscott31
    Yes, that will be great. The reason why I am asking because I am hoping to use Yeast-GEM with Escher and it seems Escher only accepts json format models.
    Moritz E. Beber
    @Midnighter
    @wtscott31 you can at any point import the SBML with cobrapy and export is as JSON.
    You might also be interested in the work to translate yeast-GEM to the BiGG identifier namespace that is happening here SysBioChalmers/yeast-GEM#188
    William Scott
    @wtscott31
    @Midnighter Thanks for pointing that out to me! I will check out that PR. I also submitted a PR to add the GPR for the genes EEB1/EHT1. Has that been added yet?