Guides & Help


Site Development and Manual

Citation

Content Summary

FAQ
1. What is KiMoSys?
2. How to Register?
3. How do I update my KiMoSys account?
4. Who can use data and models?
5. How to search and use data and associated models?
6. What kind of data are stored in KiMoSys?
7. What submission options do I have and how to submit data?
8. How to associate models with data?
9. What file formats can I submit to the KiMoSys repository?
10. Are the uploaded data and models kept private by default?
11. Can I update my data or model after submit?
12. How to delete my data and/or models?
13. Are my data and models secure?
14. Is there any example files I can use to try KiMoSys tools?
15. Is the research I put on KiMoSys citable?
16. Benefits of depositing experimental data sets and models in KiMoSys?
17. Terms and Condition of use.

Acknowledgements and Funding

Site Development and Manual

• This site is maintained and hosted by KiMoSys team at INESC-ID.

• Access to KiMoSys is granted free of charge for academic purposes. Users for commercial purpose please contact the authors before download the data sets.

KiMoSys has the following pages:

   - Home: the default page which provides the brief introduction about the platform and also main features.

   - Repository: this page helps in search and browse experimental data and associated kinetic models.

   - Tools: provides a number of operations to the first metabolic kinetic modeling steps.

   - Documentation: gives information "how to use and cite KiMoSys".

   - Links: this page provides links to other resources so that the user can get more information related to dynamic modeling.

   - Contact us: for questions, comments or suggestions.

KiMoSys is described in details in the following Manual.



Citation

Do you want to cite KiMoSys since you have referred it in your work?

Please add the following citation to your scholary references:

[1] R.S. Costa, A. Verissimo, S. Vinga, KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. BMC Systems Biology, 2014, 8:85. doi:10.1186/s12918-014-0085-3. BMC Systems Biology | PubMed


How to cite a specific data and/or associated model in KiMoSys repository?

If you use these, please cite the original article reference, and additionaly cite the data or model using a format similar to the following (typically in the "Material and Methods" section):

1) Example to reference a specific data

"The data was downloaded from KiMoSys respository http://kimosys.org [1] (November 2013, Data EntryID 30, URL: http://kimosys.org/repository/30)" (i.e., specify the date on which you downloaded the data file, Data EntryID number and the static URL to the data).


2) Example to reference a specific associated model

"The model was downloaded from KiMoSys repository http://kimosys.org [1] (November 2013, Model EntryID 13, URL: http://kimosys.org/repository/30/associated_models/13)" (i.e., specify the date on which you downloaded the model file, Model EntryID number and the static URL to the model).


How to cite your submitted data or associated model?

Be default we recommend to add the following to your manuscript:

"The data (or model) have been deposited to the KiMoSys repository (http://kimosys.org) [1] with the dataset identifier Data EntryID XX (or model identifier Model EntryID xx)."



Content summary

Organisms                                   6

Time series data of metabolites    16

Flux measurements                     10

Metabolites at seady-state           7

Enzyme / Protein concentrations   3

Associated kinetic models            14



F.A.Q.

1. What is KiMoSys?

KiMoSys is a user-friendly platform that includes a public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. It is designed to search, exchange and disseminate experimental data (and associated kinetic models) for the systems modeling community. Our mission is to promote scientific sharing and to facilitate research.

2. How to Register?

If you do not already have a KiMoSys account, create one here. Registration for the user is free and simple, having to provide a first and last name, affiliation, research interests, homepage or ORCID iD, a valid email address and a password.

3. How do I update my KiMoSys account?

Log into the KiMoSys website with your user account details. Then click 'edit user' to change your account details.

4. Who can use data and models?

Anybody can access and download public data and associated models. There are no login requirements. For more information, please read Terms and Condition of use.

5. How to search and use data and associated models?

In order to perform a term-based search, a term or a set of terms have to be entered in the Search box in the top-right part of the repository table for each data or model.
Upon open the Repository tab and clicking the corresponding EntryID the user will display the link(s) for the the data/model files. For each EntryID the user can also "Download all" (article + data files) for the data or "Download full archive" (article + data + model files) for the model.

6. What kind of data are stored in KiMoSys?

Time-series data of metabolites, metabolites at steady-state, flux data and protein levels.

7. What submission options do I have and how to submit data?

Users can contribute and submit data to the database using the manually-assisted "web platform submission" form or the "paper submission form". The submitted data will be checked by KiMoSys curators

.

Web-submission form:
1. Create a User account or Login.
2. Select Electronic Data-Submission.
3. Download the "Excel template" copy.
4. Choose appropriated data type template.
5. Complete the Excel spreadsheet template (metadata + data).
6. Fill out the web-form and upload the data file.
7. Submit the data.
8. Needs to be confirmed by a curator.
9. After the curation process the Data EntryID are marked "reviewed".
10. Curator emails the submitter to inform that the Data EntryID is "reviewed".

Quick submit form:
Alert us to publications (datasets and associated kinetic models) that we might have missed. Select Quick submit.
In this case you don´t need a KiMoSys account.

Paper submission form:
1. Download the "Excel template" copy.
2. Choose appropriated data type template.
3. Complete the Excel spreadsheet template (metadata + data).
4. Submit the data file via email to kimosys@kdbio.inesc-id.pt.
5. Fill a term of agreement and responsability.
6. We curate, assign accession number and add data to the database.

8. How to associate models with data?

Registered users can only associate kinetic model to existing data (Data Entry ID). For each Data Entry ID, you can associate several models.
1. Create a User account or Login.
2. Fill out the web-form and upload the model file(s).
3. Submit the model.
4. After the curation process the Model EntryID are marked “reviewed”.
5. Curator emails the submitter to inform that the Model EntryID is reviewed.

9. What file formats can I submit to the KiMoSys repository?

For data: structured Excel file, SBtab file (.csv), text data file (time series) for parameter estimation in COPASI.

For models: SBML, CellML, COMBINE Archive, Matlab and COPASI files.

10. Are the uploaded data and models kept private by default?

Yes. All submissions to KiMoSys repository are private by default.

11. Can I update my data or model after submit?

Yes. KiMoSys supports version control, and any stored data or model can be altered as you wish.

12. How to delete my data and/or models?

The submitter can just use the delete button when they are displayed (i.e. for data and models EntryID that have been made private). Otherwise, the submitter is not permitted to remove public shared data from KiMoSys.

13. Are my data and models secure?

All uploads that are privately stored can only be accessed by the submitter, when they are logged in.

14. Is there any example files I can use to try KiMoSys tools?

Yes. In the tools page, download a "example file" that can be used with the tools.

15. Is the research I put on KiMoSys citable?

Yes. All research made publicly available can be cited using a static URL.

16. Benefits of depositing experimental data sets and models in KiMoSys?

Your research will be highlighted and other scientists will begin using your work and citing your articles.

17. Terms and Condition of use.

KiMoSys platform is copyrighted by the team developing the resource under license GNU GPL v2. However, each individual data and model file retains the copyright assigned by the biologists that measures the data and the creators of the kinetic model, as well as the author(s) of the reference publication. Moreover, when the data (and/or model) files are shared by the submitter as public, they understand that public data (and/or model) is freely available by any other user and for any purpose under the term of the Creative Commons Attribution License. KiMoSys team not assumes responsibility for any purpose for which they are used and for copyrighted material. KiMoSys assumes that the submitter has received any necessary consent authorizations required prior to submitting the data and/or model. All users accept the risk and responsibility for the accuracy, completeness, or lack thereof, of any submitted information. In addition, any contribution to KiMoSys repository must be appropriate for sharing with the systems biology community. Access to the KiMoSys web site is granted free of charge for academic purposes. For any questions regarding our privacy or data usage policies feel free to Contact Us.



Acknowledgements and Funding

The KiMoSys team would like to thank all data and models submitters for their contributions. KiMoSys is funded by FCT and supported at present by the European Union Framework Program 7 BacHBERRY project (FP7-613793).


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