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open-life-science / ols-3

A repository for OLS-3 project leads to record their progress and assignments.
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metaNanoPype: a reproducible Nanopore python pipeline for metabarcoding #4

Open antonioggsousa opened 3 years ago

antonioggsousa commented 3 years ago

Project Lead:

Mentor:

Welcome to OLS-3! This issue will be used to track your project and progress during the program. Please use this checklist over the next few weeks as you start Open Life Science program :tada:.

Week 1 (week starting 8 February 2021): Meet your mentor!

Before Week 2 (week starting 15 February 2021): Cohort Call (Welcome to Open Life Science!)

Before Week 3 (week starting 22 February 2021): Meet your mentor!

Before Week 4 (week starting 1 March 2021): Cohort Call (Tooling and roadmapping for Open projects)

Week 5 and later

This issue is here to help you keep track of work as you start Open Life Science program. Please refer to the OLS-3 Syllabus for more detailed weekly notes and assignments past week 4.

antonioggsousa commented 3 years ago

Vision statement

We are trying to implement a flexible and reproducible pipeline for Nanopore metabarcoding data analysis. We aim to achieve this by applying different tools under the same framework and the production of a report recording all the relevant information to reproduce the analysis. We think this project can grow openly being deployed through github where the community could contribute by open new issues requesting new features or suggesting new ideas. Also more advanced users could even contribute with code doing their own pull requests to the project. We hope that through this engagement with the community the project will be more useful, updated and interesting.

katoss commented 3 years ago

Hey @antonioggsousa, I just read your vision statement and it sounds like you already have a good overview of the process and how to publish the pipeline and make it open for contributors. As someone who is not working in bioinformatics, I am wondering what your motivations are for building this pipeline, and what kinds of target groups you would like to address as contributors. That could be something to add to the vision statement. Apart from that, I find it clear and understandable :)

malvikasharan commented 3 years ago

@all-contributors please add @antonioggsousa for content

allcontributors[bot] commented 3 years ago

@malvikasharan

I've put up a pull request to add @antonioggsousa! :tada:

antonioggsousa commented 3 years ago

Hey @antonioggsousa, I just read your vision statement and it sounds like you already have a good overview of the process and how to publish the pipeline and make it open for contributors. As someone who is not working in bioinformatics, I am wondering what your motivations are for building this pipeline, and what kinds of target groups you would like to address as contributors. That could be something to add to the vision statement. Apart from that, I find it clear and understandable :)

Hi @katoss thank you for your feedback/opinion. I really appreciated. As someone that works in bioinformatics and came across this type of data a few times, I had a hard time to find a way to process it due to a lack of a user-friendly framework/pipeline integrating the several steps necessary to process the data from quality-check until annotation and diversity analyses. This also poses a problem for reproducibility. Therefore I would say that the motivation under this project is to make my life easier (and perhaps the life of others too). I would say that the target users are any user with some experience in using command-line tools that needs to process Nanopore metabarcoding data.

According to your good suggestion I tried to update my vision statement below:



Vision statement

We are trying to implement a flexible and reproducible pipeline for Nanopore metabarcoding data analysis in order to make the whole process more user-friendly for the community of researchers analyzing this type of data. We aim to achieve this by applying different tools under the same framework and the production of a report recording all the relevant information to reproduce the analysis. We think this project can grow openly being deployed through github where the community could contribute by open new issues requesting new features or suggesting new ideas. Also more advanced users could even contribute with code doing their own pull requests to the project. We hope that through this engagement with the community the project will be more useful, updated and interesting.

katoss commented 3 years ago

Hi @antonioggsousa, thank you for the explanations! I like the new version of the vision statement. The phrase on motivations makes it a lot easier to put into context for lay-persons :)

cemonks commented 3 years ago

Hey @antonioggsousa, I just read your vision statement and it sounds like you already have a good overview of the process and how to publish the pipeline and make it open for contributors. As someone who is not working in bioinformatics, I am wondering what your motivations are for building this pipeline, and what kinds of target groups you would like to address as contributors. That could be something to add to the vision statement. Apart from that, I find it clear and understandable :)

Hi @katoss thank you for your feedback/opinion. I really appreciated. As someone that works in bioinformatics and came across this type of data a few times, I had a hard time to find a way to process it due to a lack of a user-friendly framework/pipeline integrating the several steps necessary to process the data from quality-check until annotation and diversity analyses. This also poses a problem for reproducibility. Therefore I would say that the motivation under this project is to make my life easier (and perhaps the life of others too). I would say that the target users are any user with some experience in using command-line tools that needs to process Nanopore metabarcoding data.

According to your good suggestion I tried to update my vision statement below:

Vision statement

We are trying to implement a flexible and reproducible pipeline for Nanopore metabarcoding data analysis in order to make the whole process more user-friendly for the community of researchers analyzing this type of data. We aim to achieve this by applying different tools under the same framework and the production of a report recording all the relevant information to reproduce the analysis. We think this project can grow openly being deployed through github where the community could contribute by open new issues requesting new features or suggesting new ideas. Also more advanced users could even contribute with code doing their own pull requests to the project. We hope that through this engagement with the community the project will be more useful, updated and interesting.

Hi @antonioggsousa! I agree with @katoss's feedback and think this looks really clear (I'm also from way outside of this field but I understand what you're doing!). My only suggestion would be to remember the words of Yoda: 'Do or do not, there is no try'. Your project seems ambitious and exciting, and you could maybe reduce the length and increase the motivational aspect of your vision statement by removing the qualifying statements ("We are trying to", "We aim to achieve this by", "We think this project will", "We hope that", etc)?