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Process flow and guidelines
BioModels – Model submission
BioModels
Curated
Public
Non
Curated
Private
Mode
BioModels submission/curation flow https://www.ebi.ac.uk/biomodels
BioModels
Model input source
• Author
• Curator
Model Submission process
Checkpoint1
Checkpoint2
Curatoronly
Checkpoint1
• Files, Publication details etc
Checkpoint 2
• Result reproduction, annotation and curation details.
Curator/Author
curatoronly
Curator/Adm
in
Curator/Admin
!
!"
"
Model Submission Overview
Register/Login Submit
Submission
Guideline
Upload Files
Model
Information
Publication
Link
Publication
Details
Submission
Summary
Model
Submission
https://www.ebi.ac.uk/biomodels
BioModels
BioModels Home Page
BioModels
https://www.ebi.ac.uk/biomodels
New User
Existing User
Register (for new user)
BioModels
https://www.ebi.ac.uk/biomodels
* Please fill all the details and click
“Register”. You will get an email
with your login details.
Click “Help” for any query
Login (for existing users)
BioModels
https://www.ebi.ac.uk/biomodels
* Please enter the username and
password emailed to you on
registration and Click “Log In”.
You will be directed to the BioModels
Home Page again (Refer: Slide 4)
Model Submission
BioModels
https://www.ebi.ac.uk/biomodels
* Click “Submit” tab and read the submission guidelines.
* You can view details of your account like profile details, model
submitted (by you or associated people), notifications etc..
Click “Agree and Continue” to proceed to next step
Upload files
BioModels
https://www.ebi.ac.uk/biomodels
* Upload main model file for the model
* Provide details of file uploaded. Include version/build
details for better usability/portability
* Upload other additional files like base software file (e.g. *.cps for Copasi), SEDML file, experimental
input files, etc. This option provides flexibility to user to provide files that will help in model
reproducibility and thus higher citation chances. Click “Upload” to proceed.
Model Information
BioModels
https://www.ebi.ac.uk/biomodels
* Taken automatically from supported main file formats(refer Slide 6) if submitted file has these details
else need to be entered manually.
* Click “Continue” to proceed
Publication Link
BioModels
https://www.ebi.ac.uk/biomodels
* This provides drop-down option to link model with Publication Id like
PMID, DOI, URL’s, etc. Select the suitable option and click “Continue”
Publication Details
BioModels
https://www.ebi.ac.uk/biomodels
* Page information automatically get updated if Publication link is PubMed ID. For
DOI and Link, details need to be entered manually. Click “Continue” to proceed.
* Manual entry of author/s name
Submission Summary
BioModels
https://www.ebi.ac.uk/biomodels
* This page provides summary of your submission. Cross check all the information and if right
Click “Complete Submission” else click “Back” and update the correct details.
Model Submission
BioModels
https://www.ebi.ac.uk/biomodels
On submission, BioModels will provide perennial identifier which is unique biomodel id for
the model submitted. Same can be used for further database query.
Yippee.. Your model is successfully submitted to BioModels. Feel free to update your
submission any time under “My Account”.
Update submitted model
BioModels
Existing model update overview
Login My Accounts My Models
Select model
for update
Upload Files
Model
Information
Publication
Link
Publication
Details
Submission
Summary
Model
Submission
https://www.ebi.ac.uk/biomodels
BioModels
Updating existing model submission
BioModels
https://www.ebi.ac.uk/biomodels
Go to “My Account -> My Models” for list of submissions done by you
List of models submitted by
you.
Click on the model (in this case: Test Model) to get the modification options.
Updating existing model submission
BioModels
https://www.ebi.ac.uk/biomodels
Click “Update” and follow the steps given in slide 7 to slide 13. Also an additional
column “Summary of the Update” on “Submission Summary” Page (Slide 11) need
to filled to record the update history and reasons.
Submitting model modification
BioModels
https://www.ebi.ac.uk/biomodels
Once your model is update, this message will pop on webpage
Click on “Submit” button to publish the model on BioModels
Click “Confirm” to publish the model
Final message
BioModels
https://www.ebi.ac.uk/biomodels
This message confirms that your update is successful.
Logout.. and Relax.. You deserve it. See you soon.
Curation workflow
BioModels
https://www.ebi.ac.uk/biomodels
Non-curated Model
Submitted model
files
Publication Details
Analysis and Data
Extraction
Encoding model in
SBML format
Publication result
reproduction
Annotation
BioModels
Curated model
Biological and biochemical interpretation
+ mathematical representation
Model encoded in Systems biology
markup language (SBML) using reported
equations, species, parameters.
Reproducing results in the publication
Semantic enrichment by cross-
referencing model entities to known
ontologies (GO, SBO, ChEBI) and
Databases (Uniprot, Ensembl)
1
2
3
4
BioModels
Thanks…

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BioModels model demo