Second round reviews

[nselem]

• Please pay special attention to language polishing.

Reviewer Comments to Authors:
Reviewer: 1
Comments to the Author
Thank you for addressing my concerns, as well as those from the other 4 reviewers.

Reviewer: 2

Comments to the Author
General assessment
Thank you for the opportunity to read your manuscript. I acknowledge that changes have been made in response to my previous comments and thank you for additional information about the process of developing these training materials.

Your submission provides a high level overview of the features of your newly developed materials on pangenomics and the process you used to develop these materials. The manuscript is well written and easy to read. It is great to see that you have used established best practices in learning design to collaboratively develop these materials and have incorporated active learning strategies. Although I am not an expert in pangenomics, it seems that these materials are filling a training gap. There is an emphasis on catalytic and self-directed learning in this article but more context is needed to explain how this is achieved and evaluated.

The journal states that articles on areas such as education or career development must be of wide interest to the computational community. Given that the learning design methods used here are established, well documented best practices (e.g Via et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203054/ ; Wilson: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006915 ; GOBLET guidelines: https://drive.google.com/file/d/1rUiVaR8KEwF8hTq_dUCrz7ZlIk8Mx0YQ/view), I'm not sure that this story is sufficiently innovative to warrant a journal publication. It would make a wonderful conference presentation which would also serve as a way of publicising/socialising the materials with other trainers and gaining valuable feedback.

Specific areas for improvement of the manuscript in its current form

Section 2: story of the workshop

Some additional context would help strengthen your argument for the need for short format training on pangenomics.

In the paragraph that describes the Wikipedia competition there is the statement "we noticed
that although excellent materials were available, there were no public Short-format training materials.".

• Can you explain what types of materials were available and how these differed from short-format training materials? This is important context and helps strengthen your argument for the need for short format training on pangenomics.

"An important part that motivated the creation of this workshop was the difficulty we experienced when researching Pangenomics. Because of this, the development of the materials started by including the tools that we needed for our research and that we were learning."

• What difficulties did you face? The link between these difficulties and your approach is not clear.

Sections 3 and 4:

• The modular design and grading of exercises is highlighted in this section as a way of catering to learners with different skill levels and backgrounds. Can you tell us more about how these features are used to tailor the delivery of the workshop?

For example:

• There seem to be three key audiences for this workshop: biologists, mathematicians and other data scientists. Can you explain how each of these groups should use the materials?

• How did the pre-workshop surveys influence the content taught?

• How can self-directed learners use the gradings and modular structure to design their own path through the materials?

Cloud computing environment:

Great to see the use of standardised computing environments in the live workshops. This makes an enormous difference to the learner experience.

• What support is provided to self-directed learners with limited computational skills to set up and access these environments?

Section 4.2: ​​Catalytic learning is promoted during the Workshop

• Many will be unfamiliar with the concept of catalytic learning. Can you add a short definition and references to this section? Some references you might consider: Tractenberg RE. 2022 https://osf.io/preprints/socarxiv/hp4k6 ; Williams and Tractenberg et al 2023. https://doi.org/10.1371/journal.pone.0293879. This section is specifically about promoting catalytic learning (or "learning that, once completed, enables the learner to continue learning in a self-directed way" - Williams and Trachtenberg 2023) but only active learning strategies that enhance learning during the workshop are highlighted here.Which features of the workshop are specifically designed to support continued or catalytic learning?

• Is the cloud set up available to participants after the workshop to enable continued learning? #62

• If sustained learning is a goal of this workshop, how do you evaluate this? #63

Section 4.3
"This involves supporting the infrastructure, trainers, and communities that enable effective and inclusive training."

• Can you provide specific examples of how you achieve this? #64

Section 5.1

• A reference is needed for the "the alpha cycle defined by The Carpentries"

• Typos and wording #65

I have not proof read thoroughly but noticed these points:

• Section 3.2: "This data selected as a study case revisited the original first genomes with which Tettelin and collaborators [Tettelin et al., 2005]". It should be "case study" rather than "study case"

• "Pangenomic ideas are introduced in episode 1, enabling analysis by presenting a pipeline that includes public genomes downloading in episode 2" should be "Pangenomic ideas are introduced in episode 1, enabling analysis by presenting a pipeline that includes downloading public genomes in episode 2"

Reviewer: 3
Comments to the Author
The article "Multidisciplinary Workshop on Pangenomics and Topological Data Analysis" by Haydeé Contreras Peruyero, Shaday Guerrero Flores, Claudia Zirión Martínez, Paulina M. Mejía Ponce, Marisol Navarro Miranda, Jose Abel Lovaco-Flores, José María Ibarra Rodríguez, Anton Pashkov, Cuauhtemoc Licona Cassani and Nelly Selem presents a Workshop to teach Pangenomics and Topology Data Analysis.

• The main issue is that the results, in addition to be only declarative, remain rather vague: For Figure 4, it would be good to have information about how results depend on the background of participants or whether the results depend on lessons for example (i.e. +/- TDA). #66

Reviewer: 4

Comments to the Author

1. The work is generally interesting, on a workshop for pangenomics and topological data analysis. Some aspects of the workshop could perhaps have leveraged online education platforms as preparatory materials, and the range of difficulty of topics covered as part of the workshop seems somewhat broad. The organizers have done commendable work in organizing a workshop in an underrepresented area on a topic of interest, as well as to integrate aspects of active learning, divide the core content into digestible pieces of information, and ensure that learners are reflecting on the material that they are learning.

Some specific comments:

• 2) Figure 1 presents what is ultimately a relatively simple point, but the figure itself winds up being challenging to parse. I'm not sure a figure is even really necessary. #67

• I would tighten some of the background on the "Story of the Workshop" section. #68

• Introduction to the command line and an introduction to Python are at this point in time the sort of thing that could be provided to attendees in advance, perhaps with resources for interaction with others, but is not necessarily the best usage of in-person time. For that matter, it's unclear why lesson 3 doesn't occur as lesson 2. Lessons 2 and 4 are presented well.

• Figure 3 would benefit from greater explanation as to how learners are self-assessing their own proficiency as a percent score. #69