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ersilia-os / ersilia

The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
https://ersilia.io
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📑 Feature Request: Google Colab Guide #380

Closed GemmaTuron closed 1 year ago

GemmaTuron commented 2 years ago

Is your feature request related to a problem? Please describe.

We need to improve the documentation to use Google Colab. There are three main actions that could be done:

Describe the solution you'd like.

Some contributors to work together to improve this. I would suggest using a google docs to create the guides where participants can contribute. Each of the three tasks could have a leader that guides the development and then the others can contribute to it.

Describe alternatives you've considered

No response

Additional context.

No response

carcablop commented 2 years ago

@GemmaTuron Hello. I think that doing it in the GitBook of Ersilia is much better. If @Malikbadmus and @ZakiaYahya agree, I offer to upload the final version to the Gitbook.

Zainab-ik commented 2 years ago

Hello all!!

Great job, let me go part by part:

  • The document is very detailed, good job on explaining how to load data. Might I suggest we add it to Ersilia's GitBook instead of Hashnode? This is where all documentation of Ersilia resides. I think it will make it easier for other users to find, what do you think? I can give access to one of you to move the final version of the document to GitBook
  • The notebook: I like the idea of specifying the model name at the beginning as a variable. Also, I'd suggest using as much as possible the forms (as the cell for installing ersilia) where the user does not even need to see the code but just click on the button to run, or input the path or the name of the variable. I can't seem to find a link to the video, I understand this is still work in progress?

Let me know about the GitBook and thanks for the excellent work!

That's great, I thought we won't have access to the gitbook is why I suggested something similar.

Zainab-ik commented 2 years ago

Hello all!! Great job, let me go part by part:

  • The document is very detailed, good job on explaining how to load data. Might I suggest we add it to Ersilia's GitBook instead of Hashnode? This is where all documentation of Ersilia resides. I think it will make it easier for other users to find, what do you think? I can give access to one of you to move the final version of the document to GitBook
  • The notebook: I like the idea of specifying the model name at the beginning as a variable. Also, I'd suggest using as much as possible the forms (as the cell for installing ersilia) where the user does not even need to see the code but just click on the button to run, or input the path or the name of the variable. I can't seem to find a link to the video, I understand this is still work in progress?

Let me know about the GitBook and thanks for the excellent work!

Thank you very much @GemmaTuron.

@ZakiaYahya , @Zainab-ik and @carcablop . Lets us go with @GemmaTuron suggestion of adding it to Ersilia Gitbook since that will make it much easier for other user's to find.

@Zainab-ik , you can still put us through on how to use hashnode , if it wont be to much hassle for you.

That shouldn't be a problem.

thormiwa commented 2 years ago

Hello all!!

Great job, let me go part by part:

  • The document is very detailed, good job on explaining how to load data. Might I suggest we add it to Ersilia's GitBook instead of Hashnode? This is where all documentation of Ersilia resides. I think it will make it easier for other users to find, what do you think? I can give access to one of you to move the final version of the document to GitBook
  • The notebook: I like the idea of specifying the model name at the beginning as a variable. Also, I'd suggest using as much as possible the forms (as the cell for installing ersilia) where the user does not even need to see the code but just click on the button to run, or input the path or the name of the variable. I can't seem to find a link to the video, I understand this is still work in progress?

Let me know about the GitBook and thanks for the excellent work!

Thank you @GemmaTuron ... The video will be ready soon i have shared it with the team once it is ready we will share the link to it.

ZakiaYahya commented 2 years ago

@GemmaTuron Thanks for you valuable feedback. We will work on your suggestions. @carcablop i'll add the latest screenshot of variable model_name in the file, don't worry.

ZakiaYahya commented 2 years ago

@GemmaTuron Hello. I think that doing it in the GitBook of Ersilia is much better. If @Malikbadmus and @ZakiaYahya agree, I offer to upload the final version to the Gitbook.

@carcablop i'll let you know after making relevant changes in it. Then you proceed it by uploading on gitbook :)

Malikbadmus commented 2 years ago

@GemmaTuron Hello. I think that doing it in the GitBook of Ersilia is much better. If @Malikbadmus and @ZakiaYahya agree, I offer to upload the final version to the Gitbook.

@carcablop i'll let you know after making relevant changes in it. Then you proceed it by uploading on gitbook :)

You can include it in the Fetch, Serve and Predict sub-heading or what do you think?

paulinebanye commented 2 years ago

Oh just coming to GitHub! @carcablop. Thanks so much for the suggestion. Sure, I can add it to the template. There's currently a line there which says "ENSURE you include the path to your file", i can change it to something like"ENSURE you copy and paste the path to your uploaded" file

paulinebanye commented 2 years ago

@pauline-banye , on the suggestion fof @ZakiaYahya of having a global variable for the model name, instead of having to input it manually. https://colab.research.google.com/drive/1XvEil6gJGuiHdqID9jpubE9gVHcdxRUF?usp=sharing I have made the changes for that here, you can review it and incorporate it into the final design.

@pauline-banye @Malikbadmus @ZakiaYahya I also think that creating a variable for the model name is a very good idea. I suggest if it seems good to you that you can add a block specifying the name of the model, as well as the name of the path: imagen I share the link where I modify it if it can be added to the final template @pauline-banye: https://colab.research.google.com/drive/1ioD77sLNLpM62gaM0CNM-d8GVXsFKjz6#scrollTo=TYmcRRZ4mnkx

the template requires access

I'm so sorry for the late response @ZakiaYahya 🤦‍♀️. Just coming to GitHub now. We spoke about this on slack remember and it's been incorporated already 😂. Thanks so much for the suggestion

paulinebanye commented 2 years ago

@pauline-banye Sorry was unavailable yesterday but great to see that the colab feature request is set up. The thing I was finding the problem was downloading the csv file. Apart from the suggested mentions by @GemmaTuron I feel we can also introduce a prerequisite as a lot of people might be new to the colab altogether. @Zainab-ik @Malikbadmus @Cee-tech21 What say?

@sayantani11 , are you talking about the output file?

Yeah! And we should also mention the importance of SMILES format tho. A lot of people might not be aware of that🤔

Hi @sayantani11 👋, can you give me some more context regarding the output file?

Re the importance of the smiles format, should we add it to the guide or the colab template?

ZakiaYahya commented 2 years ago

@GemmaTuron i'm thinking of passing variables to input and and output paths too, so the users just have to give and define drive path just at only one place. @pauline can we incorporate changes to paths as well as i discussed with you earlier??

ZakiaYahya commented 2 years ago

@pauline i'll send you the template again with the corresponding changes

ZakiaYahya commented 2 years ago

@pauline please check the changes in this template and incorporate it final template. in this template i have pass the variables to input _path and out_path so the user have to just change the path in the starting just https://drive.google.com/file/d/1UozvLXnGluT3eZbMl2u7eKK1Sfo_s4O5/view?usp=sharing

paulinebanye commented 2 years ago

Oh just coming to GitHub! @carcablop. Thanks so much for the suggestion. Sure, I can add it to the template. There's currently a line there which says "ENSURE you include the path to your file", i can change it to something like"ENSURE you copy and paste the path to your uploaded" file

@carcablop I've adjusted that line, here's what it looks like currently. edit

paulinebanye commented 2 years ago

Hello all!!

Great job, let me go part by part:

  • The document is very detailed, good job on explaining how to load data. Might I suggest we add it to Ersilia's GitBook instead of Hashnode? This is where all documentation of Ersilia resides. I think it will make it easier for other users to find, what do you think? I can give access to one of you to move the final version of the document to GitBook
  • The notebook: I like the idea of specifying the model name at the beginning as a variable. Also, I'd suggest using as much as possible the forms (as the cell for installing ersilia) where the user does not even need to see the code but just click on the button to run, or input the path or the name of the variable. I can't seem to find a link to the video, I understand this is still work in progress?

Let me know about the GitBook and thanks for the excellent work!

Thanks for the feedback @GemmaTuron, we'll work on the additions

carcablop commented 2 years ago

adjusted that line, here's what it looks like currently.

Thank you so much @pauline-banye. This looks great. 💯

paulinebanye commented 2 years ago

adjusted that line, here's what it looks like currently.

Thank you so much @pauline-banye. This looks great. 💯

Thanks @carcablop 😄

GemmaTuron commented 2 years ago

Good job all!

@carcablop I'll follow up with you to give you access to GitBook

paulinebanye commented 2 years ago

@pauline please check the changes in this template and incorporate it final template. in this template i have pass the variables to input _path and out_path so the user have to just change the path in the starting just https://drive.google.com/file/d/1UozvLXnGluT3eZbMl2u7eKK1Sfo_s4O5/view?usp=sharing

@ZakiaYahya This is a good idea 👍 .
My only observation is that the user is restricted to one folder for both the input files and the output files. edit

Malikbadmus commented 2 years ago

@pauline please check the changes in this template and incorporate it final template. in this template i have pass the variables to input _path and out_path so the user have to just change the path in the starting just https://drive.google.com/file/d/1UozvLXnGluT3eZbMl2u7eKK1Sfo_s4O5/view?usp=sharing

@ZakiaYahya This is a good idea 👍 . My only observation is that the user is restricted to one folder for both the input files and the output files. edit

How about creating two file path variables?

drive_path_input and drive_path_output

paulinebanye commented 2 years ago

@pauline please check the changes in this template and incorporate it final template. in this template i have pass the variables to input _path and out_path so the user have to just change the path in the starting just https://drive.google.com/file/d/1UozvLXnGluT3eZbMl2u7eKK1Sfo_s4O5/view?usp=sharing

@ZakiaYahya This is a good idea 👍 . My only observation is that the user is restricted to one folder for both the input files and the output files. edit

How about creating two file path variables?

drive_path_input and drive_path_output

@Malikbadmus oh okay, in essence 3 new variables, drive_path_input, input_filename and drive_path_output

Malikbadmus commented 2 years ago

@pauline please check the changes in this template and incorporate it final template. in this template i have pass the variables to input _path and out_path so the user have to just change the path in the starting just https://drive.google.com/file/d/1UozvLXnGluT3eZbMl2u7eKK1Sfo_s4O5/view?usp=sharing

@ZakiaYahya This is a good idea 👍 . My only observation is that the user is restricted to one folder for both the input files and the output files. edit

How about creating two file path variables? drive_path_input and drive_path_output

@Malikbadmus oh okay, in essence 3 new variables, drive_path_input, input_filename and drive_path_output

Exactly.

Zainab-ik commented 2 years ago

@pauline-banye Sorry was unavailable yesterday but great to see that the colab feature request is set up. The thing I was finding the problem was downloading the csv file. Apart from the suggested mentions by @GemmaTuron I feel we can also introduce a prerequisite as a lot of people might be new to the colab altogether. @Zainab-ik @Malikbadmus @Cee-tech21 What say?

@sayantani11 , are you talking about the output file?

Yeah! And we should also mention the importance of SMILES format tho. A lot of people might not be aware of that🤔

Hi @sayantani11 👋, can you give me some more context regarding the output file?

Re the importance of the smiles format, should we add it to the guide or the colab template?

I presume the importance of the smiles format should be in the guide.

Malikbadmus commented 2 years ago

@pauline-banye Sorry was unavailable yesterday but great to see that the colab feature request is set up. The thing I was finding the problem was downloading the csv file. Apart from the suggested mentions by @GemmaTuron I feel we can also introduce a prerequisite as a lot of people might be new to the colab altogether. @Zainab-ik @Malikbadmus @Cee-tech21 What say?

@sayantani11 , are you talking about the output file?

Yeah! And we should also mention the importance of SMILES format tho. A lot of people might not be aware of that🤔

Hi @sayantani11 👋, can you give me some more context regarding the output file? Re the importance of the smiles format, should we add it to the guide or the colab template?

I presume the importance of the smiles format should be in the guide.

@Zainab-ik , I have included a section of that in the guide.

https://docs.google.com/document/d/1JlIVmLGa1cL_Qk3q1yS0hVfnDJlHupe4Zg5L8TBYG2I/edit#

paulinebanye commented 2 years ago

This is the current template, please review @GemmaTuron , @Malikbadmus , @ZakiaYahya .

I separated the drive paths to allow the user to specify the output folder. If it's preferable to specify only one drive folder, I can make some more edits.

ZakiaYahya commented 2 years ago

Hello @Gemma, @pauline-banye @Malikbadmus I have completed the work on comprehensive guide, please have a look. You can access the guide using the link: https://docs.google.com/document/d/1JlIVmLGa1cL_Qk3q1yS0hVfnDJlHupe4Zg5L8TBYG2I/edit?usp=sharing

@carcablop you can now proceed to put this guide on gitbook.

Malikbadmus commented 2 years ago

This is the current template, please review @GemmaTuron , @Malikbadmus , @ZakiaYahya .

I separated the drive paths to allow the user to specify the output folder. If it's preferable to specify only one drive folder, I can make some more edits.

@pauline-banye , Nice!!. The simplicity. And it is very well detailed. Nice work!

carcablop commented 2 years ago

Hello @gemma, @pauline-banye @Malikbadmus I have completed the work on the comprehensive guide, please have a look. You can access the guide using the link: https://docs.google.com/document/d/1JlIVmLGa1cL_Qk3q1yS0hVfnDJlHupe4Zg5L8TBYG2I/edit?usp=sharing

@carcablop you can now proceed to put this guide on gitbook.

Hello Everyone. Thanks, @ZakiaYahya. I made some spelling corrections. I tried to leave feedback on all spelling improvements. Only leave comments on the most relevant ones so as not to fill up the comments document. Also, leave a suggestion for us to consider if it can be changed. @GemmaTuron Could you give me access to Ersilia's gitbook to upload the guide? As it is the first time I will use gitbook I am following this guide. https://docs.gitbook.com/

paulinebanye commented 2 years ago

Hello @gemma, @pauline-banye @Malikbadmus I have completed the work on comprehensive guide, please have a look. You can access the guide using the link: https://docs.google.com/document/d/1JlIVmLGa1cL_Qk3q1yS0hVfnDJlHupe4Zg5L8TBYG2I/edit?usp=sharing

@carcablop you can now proceed to put this guide on gitbook.

Very well done @ZakiaYahya!! 🙌

paulinebanye commented 2 years ago

This is the current template, please review @GemmaTuron , @Malikbadmus , @ZakiaYahya . I separated the drive paths to allow the user to specify the output folder. If it's preferable to specify only one drive folder, I can make some more edits.

@pauline-banye , Nice!!. The simplicity. And it is very well detailed. Nice work!

Thanks so much @Malikbadmus 😊

GemmaTuron commented 2 years ago

Hey good job @carcablop @pauline-banye @ZakiaYahya @Malikbadmus ! @carcablop I'll follow up on slack for the gitbook access. I have pushed the template to ersilia's repo. To do it directly from colab you need to be a member of the organisation, that's why I did it instead of asking you to do it, but feel free to link my commit to your outreachy contribution: https://github.com/ersilia-os/ersilia/commit/754fbaaca77bd33849066bb3b603a23b3a71e351

ZakiaYahya commented 2 years ago

Thanks @GemmaTuron :)

Malikbadmus commented 2 years ago

Many thanks @GemmaTuron

GemmaTuron commented 1 year ago

Thanks to all contributors! I'll close this issue now

paulinebanye commented 1 year ago

Hey good job @carcablop @pauline-banye @ZakiaYahya @Malikbadmus ! @carcablop I'll follow up on slack for the gitbook access. I have pushed the template to ersilia's repo. To do it directly from colab you need to be a member of the organisation, that's why I did it instead of asking you to do it, but feel free to link my commit to your outreachy contribution: 754fbaa

Thanks so much @GemmaTuron, glad to help!