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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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Tutorial inspiration #16

Closed GemmaTuron closed 2 years ago

GemmaTuron commented 2 years ago

We are working to develop simple tutorials for the Ersilia Model Hub. Ca you comment below suggestion one example of a good tutorial from another FOSS project we could get inspiration from?

This is a required step to tackle Issue #17

julian-King22 commented 2 years ago

Does this have to include articles from blog posts? This is exciting and i would love to collaborate with you on this

Find below an example

https://towardsdatascience.com/how-to-use-machine-learning-for-drug-discovery-1ccb5fdf81ad

nangahamandine commented 2 years ago

Greetings @GemmaTuron During my esearch, I came accross this video on Youtube, I don't know if it can be of help in any way https://www.youtube.com/watch?v=SoeQZJLQlMc

nangahamandine commented 2 years ago

Below are links to some articles that I came across;

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884843/

https://www.researchgate.net/publication/256200380_Open_source_drug_discovery_-_A_limited_tutorial

https://www.simulations-plus.com/software/admetpredictor/?gclid=Cj0KCQjw0PWRBhDKARIsAPKHFGhoMZIta7SvbRDIVEYQAVqvBB1BU1CPYmbUBRPCro5zjdNiF2fDk_kaAnvpEALw_wcB

https://www.knime.com/blog/tutorials-for-computer-aided-drug-design-using-knime-workflows

nangahamandine commented 2 years ago

I'm hoping that I got the assignment correctly. In case I'm making a mistake, I'll greatly appreciate any corrections

victorabba commented 2 years ago

I think the way forward is to test the model by installing and trying it out after which we can then make a video tutorial on how newbies can install and use the model.

AishaSaman commented 2 years ago

Hi, I am Aisha and I am Outreachy internship applicant.

I think this website have really good, simple tutorials for inspiration: https://material.io/design/machine-learning/barcode-scanning.html#usage

Things that inspire me and I found helpful are:

  1. step by step with pictures and videos where necessary for better understanding
  2. dos and donts are shown with green and red colors
  3. links to related articles with each topic
  4. use cases shown
julietugo commented 2 years ago

I believe the 'Getting Started' page of Python is a good example. I would like to write such for Ersilia.

kbetty commented 2 years ago

Hello @GemmaTuron I have searched and gone through several tutorials from other FOSS communities and I found one at https://wiki.openmrs.org/display/docs/Developer+Guide so inspiring that we can borrow a leaf as we develop ours for Ersilia Model Hub and am passionate to contribute to the project.

kbetty commented 2 years ago

@GemmaTuron I think we have two separate tutorials to cater for technical contributors and non technical contributors so that we come up with tutorials that will be of great use to our community.

adeola-dev commented 2 years ago

Hi @GemmaTuron I found this helpful for the usability of the Firefox FOSS project; https://itsfoss.com/firefox/

And this for the VLC FOSS project; https://itsfoss.com/install-latest-vlc/ https://www.flexclip.com/learn/vlc.html.

I am open to collaboration with other contributors to this issue

GemmaTuron commented 2 years ago

Hello,

@AviatorIfeanyi, you link to a high level introduction to ML for drug discovery, but here we are looking at creating specific tutorials for the Ersilia Model hub, our tool. Please think how to do this and find perhaps more adapted examples before continuing

@Ama-tech0001, the first resources you list are also high level overview of using computer science for drug discovery. The most relevant and similar to what we need is the knime workflow. Good find, get your inspiration from there to work on issue #17

@victorabba a video tutorial would be fantastic!

@AishaSaman this is a good example, you can use it as a template to work on issue #17

@julietugo the "Getting Started" in python is good but very general, we would like something more detailed to the Ersilia Model Hub

@kbetty, the Developer manual is focused on new developers and contributors. Is not a bad idea but here we were thinking of tutorials for users, not developers. Can you find a user-oriented example?

@adeola-dev, you are citing great documentation of installation instructions, but here we are looking at more tutorial-type of examples, can you find one?

But to all of you, thanks for your work you are all citing interesting resources and I encourage you to answer my comments before moving to issue #17

nangahamandine commented 2 years ago

Thank you for the comments @GemmaTuron
Can you please check out what I did in issue #17 ?

kbetty commented 2 years ago

@kbetty, the Developer manual is focused on new developers and contributors. Is not a bad idea but here we were thinking of tutorials for users, not developers. Can you find a user-oriented example?

Thanks for the insight. I have gone through several user-oriented guides but the one at https://wiki.openmrs.org/pages/viewpage.action?pageId=589851 out-stands them and I think we can borrow a leaf and we come up with a user-friendly deployment guide for AI/ML models.

Kheredine commented 2 years ago

Hi @GemmaTuron , I hope this will help https://youtu.be/yL_NqXZgmks

Kcfreshly commented 2 years ago

@GemmaTuron Knime flow as suggested by @Ama-tech0001 looks great, I believe I can create a similar tutorial and possibly include a short tutorial video on how to use the Ersilia Model Hub.

Here is a sample tutorial I found

https://torchdrug.ai/docs/tutorials/

On a video tutorial, I found this material

https://www.youtube.com/watch?v=ghUyZknxq5o

In our own video tutorial, I suggest no voice, just a low background music and captions on the screen that explains each step

Onajitehub commented 2 years ago

Pictures helps as anchor to direction and it gives a visualization of what to expect as well as a road map. I would like to contribute to this project by creating a picture tutorial for users.

julietugo commented 2 years ago

Thank you @GemmaTuron for the feedback. I believe this is what you are looking for - https://towardsai.net/p/l/how-to-discover-antiviral-drugs-with-deep-learning. I can create this kind of tutorial for Ersilia

adeola-dev commented 2 years ago

Thanks @GemmaTuron for the feedback. I found the resources cited by @AishaSaman very useful. I could create a simple tutorial using the template.

MsChineme commented 2 years ago

@GemmaTuron Here is Google AutoML. Though works on the cloud, It's an open source platform that enables people with little knowledge of ML to train models specific to their use cases.

Features: Image classification Video intelligence Auto ML translation Natural language

Links https://www.youtube.com/watch?v=kgxfdTh9lz0 https://www.youtube.com/watch?v=aUfIFoMEIgg

ps-19 commented 2 years ago

@GemmaTuron mam i would love to work on this issue.

kbetty commented 2 years ago

@GemmaTuron I have been reading more about the project to gather information on how best we can develop a simple tutorials for The Ersilia Model Hub. And as from my findings there are things we need to put into consideration

  1. The users of the tutorial(Most of the users/research scientists are not computer experts).
  2. The limitation users may encounter when using the tutorials during deploying
  3. The main barriers of AI adoption in experimental research.
  4. etc

Those factors above need to be carefully analysed so that we will create a tutorial for The Ersilia Model Hub ready to use AI model which will be easier for users(researchers) to adopt.

kbetty commented 2 years ago

Getting to know more on the project, I discovered that after Ersilia AI models are validated they are published for use but they lack the Deployment feature which can aid users to use the tool(s) with ease. Of which these users most of them are scientists who are actually not computer experts and this results into our tools not being widely adopted by the users.

So the Tutorial we are developing/creating is to address the issue above. And to my understanding based on the research have curried out we are creating a Deployment feature to our AI models for users to easily adopt to the tools during their research.

@GemmaTuron let me know whether am on track as I explore more with the project?

GemmaTuron commented 2 years ago

Thanks @GemmaTuron for the feedback. I found the resources cited by @AishaSaman very useful. I could create a simple tutorial using the template.

please head to issue #17 to start working on this!

GemmaTuron commented 2 years ago

Getting to know more on the project, I discovered that after Ersilia AI models are validated they are published for use but they lack the Deployment feature which can aid users to use the tool(s) with ease. Of which these users most of them are scientists who are actually not computer experts and this results into our tools not being widely adopted by the users.

So the Tutorial we are developing/creating is to address the issue above. And to my understanding based on the research have curried out we are creating a Deployment feature to our AI models for users to easily adopt to the tools during their research.

@GemmaTuron let me know whether am on track as I explore more with the project?

Hi @kbetty, you have done a good research! Indeed, non technical users might face difficulties in using the Hub. We would like one or two slides/text/video showing how can they use it (at the current stage of deployment, which is through CLI)

GemmaTuron commented 2 years ago

@GemmaTuron Here is Google AutoML. Though works on the cloud, It's an open source platform that enables people with little knowledge of ML to train models specific to their use cases.

Features: Image classification Video intelligence Auto ML translation Natural language

Links https://www.youtube.com/watch?v=kgxfdTh9lz0 https://www.youtube.com/watch?v=aUfIFoMEIgg

Hi @MsChineme , this is a good find and a very nice example.

GemmaTuron commented 2 years ago

@GemmaTuron mam i would love to work on this issue.

Hello @ps-19, comment with some examples you will use as a template and then go ahead to issue #17 !

MsChineme commented 2 years ago

@GemmaTuron Here is Google AutoML. Though works on the cloud, It's an open source platform that enables people with little knowledge of ML to train models specific to their use cases. Features: Image classification Video intelligence Auto ML translation Natural language Links https://www.youtube.com/watch?v=kgxfdTh9lz0 https://www.youtube.com/watch?v=aUfIFoMEIgg

Hi @MsChineme , this is a good find and a very nice example.

Thank you @GemmaTuron . Do I proceed to the next step, if yes? Please what is the next step?

Rufaida98 commented 2 years ago

@GemmaTuron I think it already listed but a video tutorial as i learned a lot from video tutorials or like what you did in ersilia book to download the Ubuntu and other packages for ersilia API which was very straightforward and helpful.

kbetty commented 2 years ago

As part of the ground work during my research so that we develop a useful tutorial for users, I discovered there are as two ways of using the product:

  1. Using the CLI
  2. Using an online platform via cloud services( A web-based app)

However, at the our current stage of deployment, the user can so far use the CLI. My idea that am working on is to come up with the skeleton of a useful Table of Content for the tutorial which we can brainstorm on and then add content accordingly. cc: @GemmaTuron

ghost commented 2 years ago

We are working to develop simple tutorials for the Ersilia Model Hub. Can you comment below suggestion one example of a good tutorial from another FOSS project we could get inspiration from?

This is a required step to tackle Issue #17

Hello, I am Vaishnavi, Outreachy applicant. First, we must install the model and analyze the problems the user might encounter during installation. Then make a tutorial video which will show everything steps by step, from where to install it to how to use it.

ghost commented 2 years ago

We are working to develop simple tutorials for the Ersilia Model Hub. Can you comment below suggestion one example of a good tutorial from another FOSS project we could get inspiration from? This is a required step to tackle Issue #17

Hello, I am Vaishnavi, Outreachy applicant. First, we must install the model and analyze the problems the user might encounter during installation. Then make a tutorial video which will show everything steps by step, from where to install it to how to use it.

I found a series of tutorial videos that explain everything about the app, starting with what it is, how to use it, what plus points are, etc.

Here I am sharing this series I think this will be helpful to make any tutorial video. https://youtu.be/HCc7wzUH4ts - Introduction and app overview https://youtu.be/gH2G0niO6cM - Visualize your thoughts https://youtu.be/4sp2X4nsBwA - Tell the story through media https://youtu.be/z_H7i-ERVQI - Capture everything https://youtu.be/jq42O1W_Iys - Share for feedback https://youtu.be/oANcUP2Q9XA - Meetings with meaning

miquelduranfrigola commented 2 years ago

Hi @GemmaTuron I see a lot of traction here! Can we nominate some assignees? (see right bar).

AbiolaAnisere commented 2 years ago

We are working to develop simple tutorials for the Ersilia Model Hub. Ca you comment below suggestion one example of a good tutorial from another FOSS project we could get inspiration from?

This is a required step to tackle Issue #17

Hi @GemmaTuron,

These are a few suggestions of good tutorials I found from different sources. Please provide feedback. Thank you.

https://www.youtube.com/watch?v=SoeQZJLQlMc

https://material.io/design/machine-learning/barcode-scanning.html#usage

https://towardsai.net/p/l/how-to-discover-antiviral-drugs-with-deep-learning

https://www.youtube.com/watch?v=kgxfdTh9lz0

AbiolaAnisere commented 2 years ago

Hi @GemmaTuron,

These are a few suggestions of good tutorials I found from different sources. Please provide feedback. Thank you.

https://www.youtube.com/watch?v=SoeQZJLQlMc

https://material.io/design/machine-learning/barcode-scanning.html#usage

https://towardsai.net/p/l/how-to-discover-antiviral-drugs-with-deep-learning

https://www.youtube.com/watch?v=kgxfdTh9lz0

AnshuKumari197 commented 2 years ago

Hello, @GemmaTuron Can we make tutorial how Ersilia Model Hub will help in future for mankind ?

camus60 commented 2 years ago

@GemmaTuron @miquelduranfrigola I have gone through your documentation,specifically the strategic plan, and I have an idea of what you guys stand for and a partial vision for what you intend Ersilia to become.

In light of that, I believe your tutorials should be modeled more like a mini-course similar to the ones in the links below

I would argue that it would be much easier to grow a tutorial organically as a course over-time and would capture all of Ersilia's values.

https://huggingface.co/course/chapter1/1

https://spacy.io/usage/spacy-101

or,create mini-projects using Ersilia's models the structure could be similar to the link attached by a fellow community member

https://www.youtube.com/watch?v=kgxfdTh9lz0

I can come up with something similar.

GemmaTuron commented 2 years ago

Hello all,

Thanks for your ideas, sound great! Please follow the new contribution guidelines to make sure we can track each applicant's work and suggestions!

I will close this issue now to move the discussions to the relevant thread