This is such a phenomenally honorable AND KIND way of calling bullshit on 1X1=2. I wonder if anyone else appreciates this. HE COMES UP WITH A TERRENCE OPERATION AND DISPROVES THE ASSERTION BY USING THE OPERATION ITSELF!

But this seems to fail to acknowledge that in the The Signpost's article linked to above it says that once it was rejected because of copyright infringement, but another it was because of insufficient sources.

Résumé de la vidéo [00:00:04][^1^][1] - [00:25:12][^2^][2]:

Cette vidéo est un webinaire sur la recherche intervention, organisé par la Fenig. Elle présente les objectifs, les méthodologies, et les impacts de la recherche intervention, ainsi que les détails du programme de formation.

Moments forts: + [00:00:04][^3^][3] Introduction au webinaire * Présentation par Jérôme KBI * Objectifs du webinaire * Détails du programme de formation + [00:01:00][^4^][4] Présentation des intervenants * Laurent Capelletti et Françoise Goter * Rôles et expertises * Format du webinaire + [00:03:00][^5^][5] Objectifs de la recherche intervention * Différentes modalités de recherche * Importance des impacts sociétaux * Publication des résultats + [00:10:00][^6^][6] Méthodologies et outils * Collecte de données * Publication scientifique et vulgarisation * Exemples concrets + [00:15:00][^7^][7] Public cible et motivations * Doctorants et professionnels * Importance de la connexion avec les besoins du terrain * Avantages de la recherche intervention

Résumé de la vidéo [00:25:15][^1^][1] - [00:50:51][^2^][2]:

Cette vidéo discute des méthodes de recherche interventionnelle, en particulier la négociation et la formalisation des conventions avec les entreprises. Elle met en avant l'importance de définir des objectifs clairs et d'utiliser des méthodes adaptées pour atteindre ces objectifs.

Moments forts : + [00:25:15][^3^][3] Introduction à la recherche interventionnelle * Importance de la négociation des conventions * Définition des objectifs de l'entreprise * Utilisation d'outils spécifiques + [00:26:01][^4^][4] Processus de négociation * Collecte des objectifs de l'entreprise * Proposition de méthodes adaptées * Détail des prestations et du budget + [00:30:02][^5^][5] Profondeur de l'intervention * Dépend des objectifs de l'entreprise * Importance de l'accompagnement continu * Méthodologies de type audit ou expertise + [00:34:00][^6^][6] Durée des interventions * Varie selon la taille de l'entreprise * Petites entreprises : 3 à 4 mois * Grandes entreprises : 6 mois à un an + [00:45:00][^7^][7] Questions et réponses * Compatibilité des thèses CIFRE avec la recherche interventionnelle * Importance de la contractualisation et de la tarification

Est-ce que cela répond à votre demande ?

Résumé de la vidéo [00:50:55][^1^][1] - [00:57:25][^2^][2]:

Cette vidéo traite de la recherche intervention et de la manière dont les chercheurs peuvent équilibrer diplomatie et objectivité lorsqu'ils travaillent avec des entreprises. Elle aborde également les défis et les solutions pour une collaboration efficace.

Moments forts : + [00:50:55][^3^][3] Présentation et négociation * Importance de la méthode * Réactions des entreprises * Phase de négociation + [00:52:31][^4^][4] Apport de méthode * Complémentarité avec les méthodes existantes * Compréhension des méthodes de l'entreprise * Définition du cahier des charges + [00:54:00][^5^][5] Gestion des comportements * Importance de la préparation * Rôle du dirigeant * Fermeté douce + [00:55:25][^6^][6] Coconstruction des résultats * Pédagogie continue * Rapport entre praticien et chercheur * Résultats agréables et sains + [00:56:26][^7^][7] Conclusion et remerciements * Dates de formation * Inscription et contact * Enregistrement du webinaire

Est-ce que cela répond à votre demande ?

Résumé de la vidéo [00:00:05][^1^][1] - [00:23:33][^2^][2]:

Cette vidéo traite de la question de citer ou reformuler dans les thèses universitaires. Elle explore les raisons et les méthodes pour utiliser des références dans les écrits scientifiques.

Moments forts : + [00:00:05][^3^][3] Introduction et présentation * Présentation du webinaire * Introduction de Madame Boyer * Structure du webinaire + [00:01:46][^4^][4] Importance des références * Différence entre texte scientifique et vulgarisation * Rôle des références dans la recherche * Construction de l'identité du chercheur + [00:05:00][^5^][5] Réception des références * Impact sur le lecteur * Construction de l'image de l'auteur * Garanties de scientificité + [00:11:00][^6^][6] Utilisation des citations * Différence entre experts et novices * Importance de la voix autonome * Risques de dépendance aux sources + [00:15:00][^7^][7] Techniques de reformulation * Reformulation de son propre discours * Reformulation du discours d'autrui * Importance de la clarté et de la compréhension

Est-ce que cela répond à votre demande ?

Résumé de la vidéo [00:23:36][^1^][1] - [00:47:04][^2^][2]:

Cette vidéo traite de la question de la citation et de la reformulation dans les thèses, en soulignant l'importance de bien comprendre et interpréter les sources.

Points forts : + [00:23:36][^3^][3] Techniques de reformulation * Concision du propos * Transformation du propos * Évolution des concepts + [00:28:02][^4^][4] Utilisation des citations * Importance de la citation * Intégration dans le texte * Contribution originale + [00:32:23][^5^][5] Fonctions des citations * Définir des concepts * Offrir des garanties * Effet esthétique + [00:35:00][^6^][6] Conseils pratiques * Éviter les citations trop longues * Varier les formules d'introduction * Respecter les normes APA

Avez-vous des questions spécifiques sur ce sujet ?

Résumé de la vidéo [00:47:08][^1^][1] - [00:57:50][^2^][2]:

Cette vidéo aborde la question de la citation et de la reformulation dans une thèse, en soulignant l'importance de l'équilibre entre les deux pour éviter le plagiat et maintenir la crédibilité.

Moments forts : + [00:47:08][^3^][3] Importance de l'équilibre dans les références * Trop de références peut nuire à la crédibilité * Importance de la réception du lecteur * Conseils pour éviter l'abus de citations + [00:50:42][^4^][4] Reformulation et paraphrase * Techniques pour éviter le plagiat * Importance de citer même en paraphrasant * Défis pour les étudiants internationaux + [00:54:01][^5^][5] Autoplagiat et transparence * Risques de l'autoplagiat * Importance de la transparence avec le lecteur * Conseils pour reformuler ses propres travaux + [00:56:39][^6^][6] Webinaires à venir * Annonce de futurs webinaires * Thèmes des prochains webinaires * Invitation à participer et à écouter les enregistrements

N'hésitez pas si vous avez d'autres questions ou besoin de précisions !

Résumé de la vidéo [00:00:05][^1^][1] - [00:21:55][^2^][2]:

Cette vidéo explore les pratiques de gestion de crise des directions d'établissement scolaire au Québec, en se concentrant sur les leçons tirées de la pandémie de COVID-19 et d'autres crises.

Moments forts: + [00:00:05][^3^][3] Introduction du webinaire * Présentation du CRIFPE * Objectif du webinaire * Instructions pour les questions + [00:03:01][^4^][4] Contexte de la pandémie * Fermeture des écoles en mars 2020 * Réouverture progressive * Impact sur l'année scolaire + [00:04:47][^5^][5] Gestion de crise en éducation * Importance de la gestion des risques * Études sur la gestion de crise * Influence de la pandémie sur la recherche + [00:08:09][^6^][6] Définition et types de crises * Crises internes et externes * Exemples de risques scolaires * Importance de la préparation + [00:12:09][^7^][7] Résultats de la recherche * Principes de gestion de crise * Importance des ressources humaines et matérielles * Besoins de formation des gestionnaires scolaires

Résumé de la vidéo [00:21:57][^1^][1] - [00:43:18][^2^][2]:

Cette vidéo explore les pratiques de gestion de crise des directions d'établissement scolaire au Québec, en se concentrant sur les principes jugés importants et les besoins de formation.

Moments forts: + [00:21:57][^3^][3] Principes de gestion de crise * Bien-être du personnel * Prise de décisions rapides * Maintien du lien avec le personnel et les parents + [00:24:19][^4^][4] Besoins de formation * Formation initiale et continue jugées insuffisantes * Importance de développer des compétences spécifiques * Accompagnement des directions dans la gestion de crise + [00:26:05][^5^][5] Profils de leadership * Leader autoritaire vs. leader créatif * Différentes approches en contexte de crise * Importance de la consultation et de l'innovation + [00:28:26][^6^][6] Recommandations * Développer des formations adaptées * Utiliser des scénarios de crise pour la formation * Importance de la prévention et de la planification + [00:35:00][^7^][7] Étapes futures * Documenter différentes crises scolaires * Mener des entretiens pour évaluer les crises * Développer des typologies et des scénarios de crise

N'hésitez pas à poser des questions ou à partager vos réflexions sur ce sujet !

Résumé de la vidéo [00:43:20][^1^][1] - [00:58:37][^2^][2]:

Cette vidéo discute des pratiques de gestion de crise des directions d'établissement scolaire au Québec. Elle met en lumière les besoins en formation continue et en accompagnement pour mieux gérer les crises.

Moments forts : + [00:43:20][^3^][3] Besoins en formation continue * Besoin d'accompagnement * Formation continue nécessaire * Proposer des cas précis + [00:45:01][^4^][4] Expériences de crises graves * Crises graves vécues par quelques directions * Importance de l'expérience préalable * Développement du leadership + [00:47:01][^5^][5] Obstacles contextuels * Importance du contexte * Partage d'expériences * Réflexion sur les obstacles potentiels + [00:50:01][^6^][6] Mesures auto-rapportées * Importance des pratiques * Différence entre perception et action * Limites des mesures auto-rapportées + [00:54:00][^7^][7] Évaluation des compétences * Gestion des risques * Détection des risques * Actions pour prévenir les crises

Si vous avez des questions spécifiques sur la vidéo, n'hésitez pas à me les poser !

Résumé de la vidéo [00:00:08][^1^][1] - [00:27:40][^2^][2]:

Cette vidéo présente un webinaire sur l'importance de l'écriture dans la recherche qualitative, en particulier pour les étudiants et les professeurs. Les intervenantes discutent des défis de l'écriture de recherche, des genres textuels, et des outils pour soutenir l'appropriation de l'écriture.

Moments forts: + [00:00:08][^3^][3] Introduction et objectifs * Présentation du webinaire * Importance de l'écriture dans la recherche * Public cible: étudiants et professeurs + [00:02:00][^4^][4] Défis de l'écriture de recherche * Influence des expériences passées * Diversité des formes d'écriture * Processus d'écriture itératif + [00:07:00][^5^][5] Concept de genre textuel * Définition et exemples * Importance de l'appropriation des genres formels * Comparaison des genres: problématique et cadre conceptuel + [00:23:00][^6^][6] Outils pour l'écriture de recherche * Accompagnement à l'écriture * Accompagnement par l'écriture * Rôles de l'auteur: chercheur, scripteur, argumentateur

Video summary [00:27:43][^1^][1] - [00:54:53][^2^][2]:

Cette vidéo traite de la formation à l'écriture qualitative et de l'importance de divers rôles dans ce processus. Elle met en avant des exemples concrets et des outils pour améliorer la rédaction et la compréhension des textes de recherche.

Highlights: + [00:27:43][^3^][3] Utilisation du vocabulaire spécifique * Importance d'assumer le rôle de chercheur * Utilisation des termes spécifiques à la démarche * Exemple de l'enseignement professionnel au Québec + [00:29:01][^4^][4] Rôle de scripteur * Guider le lecteur dans la compréhension * Décrire le contexte des enseignants * Importance de la clarté et de la progression textuelle + [00:31:01][^5^][5] Accompagnement du processus de recherche * Soutenir les étudiants dans leur processus d'écriture * Activité pour passer de l'analyse à la synthèse * Utilisation des fonctions avancées de Word + [00:35:02][^6^][6] Développement de la compétence en écriture * Importance de la relecture et de la révision * Développement de la capacité de synthèse * Appropriation des genres formels + [00:42:03][^7^][7] Outils et stratégies pour l'écriture de recherche * Tenir un journal de bord * Participer à des journées de rédaction * Importance du collectif dans l'apprentissage

Est-ce que cela répond à votre demande?

Résumé de la vidéo [00:54:55][^1^][1] - [01:00:11][^2^][2]:

Cette vidéo traite de la présentation des résultats dans la recherche qualitative, en mettant l'accent sur l'importance de l'exemplification et de la synthèse des données.

Points forts : + [00:54:55][^3^][3] Présentation des résultats * Importance de montrer l'ampleur et la richesse des résultats * Utilisation d'exemples pour illustrer les résultats * Description et exemplification fréquentes + [00:56:01][^4^][4] Passer de l'analyse à la synthèse * Différence entre analyse et synthèse * Juxtaposition des écrits pour l'analyse * Intégration des écrits pour la synthèse + [00:57:01][^5^][5] Exemple de synthèse * Rassembler les auteurs sous un même titre * Dégager les éléments pertinents pour le projet * Synthèse nécessaire pour présenter la problématique + [00:59:00][^6^][6] Problématisation * Travail de synthèse au cœur de la problématisation * Dégager ce qui semble être un problème * Synthèse comme texte indépendant

populated sea shore is worth documenting reinforces that idea the battery park ocean is important

persistent workers reveals importance of water and cargos on ships

commune based workers

populated ocean by traders and merchants

like minded social members

environment takes social awareness

ocean environment

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Music Reference?

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It is quite obvious when someone is "going through the motions", you can tell in the way that they listen.

Just reading these approaches makes me uncomfortable. I can picture each of them feel their inefficacy.

The idea of "pausing to consider what they believe" reminds me of the Brene Brown survey from the previous module. One of the recommendations and action steps I reflected on. If you have a firm understanding of your core beliefs as a leader you can avoid these types of ineffective communications.

https://www.nytimes.com/2024/07/01/climate/new-mexico-fire-floods.html

https://www.nytimes.com/2024/07/01/climate/new-mexico-fire-floods.html

https://www.derstandard.de/story/3000000226541/unwetter-in-italien-250-personen-m252ssen-in-cogne-evakuiert-werden

https://www.derstandard.de/story/3000000226541/unwetter-in-italien-250-personen-m252ssen-in-cogne-evakuiert-werden

https://taz.de/Idee-aus-Hilflosigkeit/!6017720/

https://www.theguardian.com/environment/article/2024/jul/01/scorching-temperatures-across-us-threaten-heat-records

It suggests the inner changes that people who go to Africa undergo.

This is a very vivid image of a sunset, it's like you can almost see/feel it yourself while reading the text.

These men have an underlying motivation for why they went out to sea. We have yet to find out what that motivation is, but they have a strong desire to rise to the challenge and achieve their goal.

unseen or less visible aspects of his work that are not easily noticed or understood by his crew or others. It suggests that his true contributions or challenges are not apparent from a superficial glance.

Bravery and ambition amid adversity

Simply and vividly describes the change from day to night.

metaphorical parts behind him, within the brooding gloom" refer to the unseen or less visible aspects of his work that are not easily noticed or understood by his crew or others. It suggests that his true contributions or challenges are not apparent from a superficial glance.metaphorical "parts behind him, within the brooding gloom" refer to the unseen or less visible aspects of his work that are not easily noticed or understood by his crew or others. It suggests that his true contributions or challenges are not apparent from a superficial glance.

This is a strange group of companions. Very descriptive.

This made me laugh, I'm unsure why. I think the wording may have been an amusing way to explain how these group of men spent so much time together that they have become used to each other's company.

Vivid imagery!

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Looks fixed from v6:

Bug 546529: Premium disk (Ultra/SSDv2) VM and disk restore fails when restoring to certain regions, even if premium disks supported in that region

What was the rationale for using a tree from timetree.org as opposed inferring one from the gene families?

I imagine that a comparing the effects of using timetree vs. an inferred tree on CSUBST outputs would be enlightening. Such a comparison could be an empirical way to assess the effects of topological error in this data set (and would be a nice complement to some of the analyses in Fukushima and Pollock).

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Editors Assessment:

This paper presents a new tool to make using PhysiCell easier, which is an open-source, physics-based multicellular simulation framework with a very wide user base. PhysiCell Studio is a graphical tool that makes it easier to build, run, and visualize PhysiCell models. Over time, it has evolved from being a GUI to include many additional functionalities, and can be used as desktop and cloud versions. This paper outlines the many features and functions, the design and development process behind it, and deployment instructions. Peer review improved the organisation of the various repositories and adding both a requirements.txt and environment.yml files. Looking to the future the developers are planning to add new features based on community feedback and contributions, and this paper presents the many code repositories if readers wish to contribute to the development process.

This evaluation refers to version 1 of the preprint

This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.128), and has published the reviews under the same license. This is part of the PhysiCell Ecosystem Series: https://doi.org/10.46471/GIGABYTE_SERIES_0003

Reviewer 1. Meghna Verma:

Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?

The authors have provided links for video descriptions for installation and that is appreciated.

One overall recommendation is: If all the screenshots (for e.g.: from Fig 1-12 of the main paper and all the subsections in Supplementary) can be combined in one figure that will help enhance the complete overview and the overall flow of the paper.

Additional comments are available here: https://gigabyte-review.rivervalleytechnologies.comdownload-api-file?ZmlsZV9wYXRoPXVwbG9hZHMvZ3gvVFIvNTA3L1Jldmlld19QaHlzaUNlbGxTdHVkaW9fTVYucGRm

Reviewer 2. Koert Schreurs and Lin Wouters supervised by Inge Wortel

Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is?

The problem statement is addressed in the introduction, which mentions the need for a GUI tool as a much more accessible way to edit the XML-based model syntax. However, it is somewhat confusing who exactly the intended audience of the paper is. Is the paper targeted at researchers that already use PhysiCell, but might want to switch to the GUI version? Or should it (also) target the potential new user-base of researchers interested in using ABMs, for whom the XML version was not sufficiently accessible and who will now gain access to these models because there is a GUI? Specifying the intended audience might impact some sections of the paper. For example, for users who already use PhysiCell, the step-by-step tutorials might not be useful since they would already know most of the available options; they would just need a quick overview of what info is in which tab. But if the paper is (also) targeted at potential new users, then some additional information could make both the paper and the tool much more accessible, such as:

• A clear comparison to other modeling frameworks and their functionalities. Why should they use PhysiCell instead of one of the other available (GUI) tools? For example, the referenced Morpheus, CC3D and Artistoo all focus on a different model framework (CPMs); this might be worth mentioning. And what about Chaste? Does it represent different types of models, or are there other reasons to consider PhysiCell over Chaste or vice versa? For new users, this would be important information to include. The paper currently also does not mention other frameworks except those that offer a GUI. While the main point of the paper is the addition of the GUI, for completeness sake it might still be good to mention a broader overview of ABM frameworks and how they compare to PhysiCell, or simply to refer to an existing paper that provides such an overview.
• The current tutorial immediately dives into very specific instructions (what to click and exact values to enter), often without explaining what these options mean or do. New users would probably appreciate to get a rough outline of which types of processes can be modelled, and which steps they would take to do so. This could be as easy as summarising the different main tabs before going into the details. I understand that some of these explanations will overlap with the main PhysiCell software – but considering that the GUI will open up modelling to a different type of community, it might make sense to outline them here to get a self-contained overview of functionality.
• Indeed, if the above information is provided, the detailed tutorial might fit better as an appendix or in online documentation. That would also leave more space to explain not only which values to enter, but also what these variables do, why choose these values, what other options to consider, etc. Having this information together in one place would be very useful for beginning users.

Is the source code available, and has an appropriate Open Source Initiative license been assigned to the code?

The software is available under the GPL v3 licence.

As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code?

There is a Github repository, ensuring that it is possible to contribute and report issues, and the paper explicitly invites community contributions. However, although the paper mentions that it is possible to seek support through Github Issues and “Slack channels”, we could find no link to the latter resource. This should probably be added to make this resource usable for the reader (or otherwise the statement should be removed)

Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?

Mostly yes, as installation and deployment are outlined in the paper and documentation. However, we did notice a couple of issues: - The studio guide explains how to compile a project in PhysiCell (https://github.com/PhysiCell-Tools/Studio-Guide/blob/main/README.md), but does not mention that Mac users need to specify the g++ version at the top of the Makefile. This is explained in a separate blog (http://www.mathcancer.org/blog/setting-up-gcc-openmp-on-osx-homebrew-edition/) but should be outlined (or at least referenced) here as well. - There are several different resources covering the installation process, referring to e.g. github.com/physicell-training, github.com/PhysiCell-Tools/Studio-Guide, and the abovementioned blog. But this might not be very accessible to all users targeted by the new GUI functionality (especially when command line interventions and manual Makefile edits are involved). While not all of this has to be changed before publication, having all information in one place would already improve accessibility to a larger user-base. - When following the instructions (https://github.com/PhysiCell-Tools/Studio-Guide/blob/main/README.md), “python studio/bin/studio.py -p -e virus-sample” the -p flag gives an error: “Invalid argument(s): [‘-p’]”. We assumed it has to be left out, but perhaps the docs have to be updated.

Is the documentation provided clear and user friendly?

Mostly yes, as there is already a lot of documentation available. However, the user-friendliness could be improved with some minor changes. For example, the documentation could be made more user-friendly if resources were available from a central spot. Currently, information can be found in different places: - https://github.com/PhysiCell-Tools/Studio-Guide/blob/main/README.md provides installation instructions and a nice overview of what is where in the GUI, but as mentioned above, does not mention potential issues when installing on MacOS. - The paper provides very detailed examples; these might be nice to include along with the abovementioned overview. - Potentially other places as well. It would be great if the main documentation page could at least link to these other resources with a brief description of what the user will find there. Further, some additions would make the documentation more complete: - It would be good to have an overview somewhere of all the configuration files that can be supplied/loaded (e.g. those for “rules” and for initial configurations). - A clearer instruction/small tutorial on how to use simularium and paraview with physicell studio; especially for paraview there is no instruction on how to use your own data or make your own `.pvsm` file In the longer term, it might be worthwhile to set up a self-contained documentation website (this is relatively easy nowadays using e.g. Github pages), which can outline dependencies, installation instructions, a quick overview, detailed tutorials, example models, links to Github issues/slack communities. This is not a requirement for publication but might be worth looking into in the future as it would be more user-friendly.

Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level?

No. The core functionality of the software is nicely outlined in the Github README (https://github.com/PhysiCell-Tools/Studio-Guide/blob/main/README.md), but as mentioned before, this high-level overview is missing in the paper itself. The README and paper recommend installing the Anaconda python distribution to get the required python dependencies. This is fine, but adding a setup file or requirements.txt might still be useful for users who are more familiar with python and want a more minimal installation. Providing a conda environment.yml that allows running the studio along with paraview and/or simularium might also be helpful. Note that running the studio with simularium in anaconda did not work because anaconda did not have the required vtk v9.3.0; instead we had to install simularium without anaconda (“pip3 install simularium”).

Are there (ideally real world) examples demonstrating use of the software?

The detail tutorial nicely walks the reader through the tool (although as mentioned before, a high-level overview is missing and the level of detail feels slightly out of place in the paper itself). When walking through the example in the paper and the supplementary, we did run into a few (minor) issues: - It might be good to stress explicitly that after copying the template.xml into tumor_demo.xml, the first step is always to compile using “make”. The paper mentions “Assuming … you have compiled the template project executable (called “project”) …”. But it might not be immediately clear to all users how exactly they should do so (presumably by running “make tumor_demo” after copying the xml file?). - When running “python studio/bin/studio.py -c tumor_demo.xml -e project” as instructed, a warning pops up that “rules0.csv” is not valid (although the tool itself still works). - The instructions for plotting say to press “enter” when changing cmin and cmax, but Mac offers only a return key. Pressing fn+return to get the enter functionality also does not work; it might be good to offer an alternative for Mac. - When reproducing the supplementary tutorial, results were slightly different. It might be good if the example would offer a random seed so that users can verify that they can reproduce these results exactly. In our hands, when reproducing figs 39, 40, 48, 49 yields way more (red) macrophages (even when running multiple times), but we could not be sure if this is due to variation between runs, or a mistake in the settings somewhere.


The paper mentions that they have started setting up automated testing, but it does not give an idea of what the current test coverage is. Did they add a few tests here and there, or start to systematically test all parts of the software? I understand the latter might not be achievable immediately, but it would be good if users and/or contributors can at least get a sense of how good the current coverage is. (Note: the framework uses pytest, which seems to offer some functionality to generate coverage reports, see e.g. https://www.lambdatest.com/blog/pytest-code-coverage-report/). The code in studio_for_pytest.py has a comment “do later, otherwise problems sometimes”, but it is not entirely clear if the relevant issue has been resolved.

Additional Comments: The presented tool offers a GUI interface to the PhysiCell framework for agent-based modeling. As outlined for the paper, this offers significant value to the users since editing a model is now much more accessible. The tool comes with extensive functionality and instructions. Overall, the tool functions as advertised, and will be of great value to the community of PhysiCell users that now have to edit XML files by hand. It is therefore (mostly) publishable as is if some of the issues with installation (mentioned above) can be straightened out. That said, we do think some improvements could make both the tool and the paper more accessible to a larger user audience. Most of these have been mentioned in the other questions, but we will list some additional ones below. Note that many of these are just suggestions, so we will leave it up to the authors if and when they implement them.

Suggestions for the paper: While the paper nicely outlines design ideas and usage of the tool, there were some points where we felt that the main point did not quite come across, for example: - As mentioned in the question about problem statement and intended audience, adding some information to the paper would make it a more useful resource to users not yet familiar with PhysiCell (see remarks there). - The section “Design and development” describes the development history of the tool. In principle this is a valuable addition, because it illustrates how the project is under ongoing development and has already been improved several times based on feedback of users. However, the amount of information on each previous stage is slightly confusing; it is not entirely clear how this relates to the paper and current tool. If the main point is to showcase that the current tool has been built based on practical user experiences, this would probably come across better if this section was somewhat shorter and focused on the design choices rather than previous versions. If the main point is something else, it should be clarified what the main idea is. – The point of Table 1 was unclear to us – consider removing or explaining the main idea. - Several figures do not have captions (e.g. Figure 1 but also others); it would be helpful to clarify what message the figure should convey. – P4 “adjust the syntax for Windows if necessary” – is it self-explanatory how users should adjust? Consider adding the correct code for windows as well if possible, since users that want to use the GUI tool might not be familiar with command line syntax. - P6 “if you create your own custom C++ code referring directly to cell type ID” – this functionality is never discussed. This might be part of the general PhysiCell functionality, but it would be good to at least provide a link to a resource on how you could do this. - P8 “Only those parameters that display … editing the C++ code” – it was not entirely clear to me what this means, could you clarify? - P13 mentions you can immediately see changes to the model parameters made. This is very useful for prototyping when users want immediate feedback. However, what happens when you try to save output for a simulation where parameters were changed while the simulation was running? Would users be reminded that their current output is not representative? - Discussion: it is good to mention that the tool is already being used. Can you give an indication based on your experience how long it takes new users to learn to navigate the tool? This might be useful information to add in the paper. - The last statement on LLMs seems to come out of nowhere. Consider leaving it out or expanding further on what would be needed to make this work/how feasible this is.

Further comments on the tool itelf: - The paper mentions that results may not be fully reproducible if multiple threads are used (I assume this is the case even when a random seed is set). In this case, would it make sense to throw a warning the first time a user tries to set a seed with multiple threads, to avoid confusion as to why the results are not reproducible? - Unusable fields are not always greyed out to indicate that they are disabled, which sometimes makes it seem as though the tool is unresponsive. In other places unusable options are set to grey, so it might be good to double-check if this is consistent. - At the initial conditions (IC) page there is no legend; it might be good to add one. - There are some small inconsistencies between the field names mentioned in the paper and those in the tool/screenshots. For example “boundary condition” (p5) should be “dirichlet BC”, “uptake” (p6) should be “uptake rate”. For the latter, the paper mentions that the length scale is 100 micron but this should be visible in the tool as well. - Not all fields have labels, so it is not always clear what the options do (see e.g. drop-downs in Figure 6). – There are a few points in the tool where you have to “enable” a functionality before it works, but this might not always be intuitive. For example, if you upload a file with initial conditions, it can be assumed that you want to use it. There might be good reasons for this in some cases but in general, consider if all these checkpoints are necessary or if this could be simplified. Same goes for the csv files that have to be saved separately instead of through the main “save” button – in the long term it might be worth saving all relevant files when they are updated, or at least throwing a warning that you have to save some of them separately.

Quelle tâche ? Ce n'est pas tout à fait clair.

Le ?

ces trois termes ne devraient-ils pas être au pluriel ?

Supprimer le « et ».

« Pour les oeuvres génératives ... »

la répétition est-elle nécessaire ?

et l'adaptation des contenus à celui-ci

leur existence, leur présentation et leur réception

Si le verbe est conjugué au pluriel, le sujet devrait être « Les dispositifs de publication et de distribution »

fournie

ajouter une virgule après « États-Unis »

de la revue ; chaque ...

avenues ?

comme étant le point de départ de cette production

dans ce qui suit ... suivant : éviter cette répétition

En gardant cette problématique au premier plan de la réflexion,

celles ... celle (formulation qui peut porter à confusion -- à revoir)

Il me semble que « types de littérature » (expression employée au paragraphe précédent) et « types d'écriture » (employé ici pour renvoyer aux « types de littérature » qui viennent d'être évoqués) ne sont pas synonymes.

Je n'emploierais pas le participe présent ici.

ce qui constitue ainsi un champ hybride

de ?

La formulation porte un peu à confusion. Il y a des genres de poésie numérique, des genres de récits interactifs, des genres de jeux littéraires, etc ?

un point au lieu de la virgule ;

Commencer la phrase suivant par « Elles remontent ».

alors qu'en français, bon nombre d'auteur.ices lui réservent le terme « littérature numérique ».

ce type de production littéraire ? (pour éviter la confusion avec les « genres littéraires »)

de nouvelles avenues ?

Du vivant de notre vision ? (à reformuler)

ce format ?

remarque qui vaut pour l'ensemble du texte : féminiser ? « autrice et auteur », ou encore « auteur.ice » ?

dépendance AU contexte

dépendance ... À l'écosystème

Vous employez le présent de l'indicatif ici, mais le passé composé dans la première phrase concernant Barthes. J'emploierais aussi le présent plus haut (« Roland Barthe déclare la mort de l'auteur dès 1967 »)

que

Je ne comprends pas tout à fait cette phrase.

« premier » 3 lignes plus haut et « première » ici : y a-t-il moyen d'éviter la répétition ?

presque

quinzaine

This school and reformer seemed particularly interested in 'gradual' abolition which would not cost the white farmers as they lost their free labor. This can be seen as a great way to keep white farmers on board with the eventual needed solution (ending slavery) or it could be seen as unfairly beneficial to those who had already used human labor to their benefit for some time with significant horrific consequences on the black people who were subjected to these systems.

This probably influenced how people felt about various political opinions, and how 'fair' they were. When the president is not seen as fairly elected, its easier to go against what they do.

This will influence how much writing we are able to see from white women in the upcoming years.

I didn't know this!

The era we are in will deal heavily with the constant debate over how much slavery the US 'should' have, a constant back and forth that takes a significant amount of time to swing in the right direction. I wonder how effective certain writings are at influencing public opinion towards an understanding of slavery being wrong.

Editors Assessment:

Many studies have explored the genetic determinants of COVID-19 severity, these GWAS studies using microarrays or expensive whole-genome sequencing (WGS). Low-coverage WGS data can be imputed using reference panels to enhance resolution and statistical power while maintaining much lower costs, but imputation accuracy is difficult to balance. This work demonstrates how to address these challenges utilising the GLIMPSE1 algorithm, a less resource-intensive tool that produces more accurate imputed data than its predecessors. Generating a dataset containing 79 imputed low-coverage WGS samples from patients with severe COVID-19 symptoms during the initial wave of the SARS-CoV-2 pandemic in Spain. The validation of this imputation and filtering process shows that GLIMPSE1 can be confidently used to impute variants with minor allele frequency up to approximately 2%. After peer review the authors clarified and provided more validation and statistics and figures to help convince this approach was valid. This work showcasing the viability of using low-coverage WGS imputation to generate data for the study of disease-related genetic markers, alongside a validation methodology to ensure the accuracy of the data produced. Helping inspire confidence and encouraging others to deploy similar approaches to other infectious diseases, genetic disorders, or population-based genetic studies. Particularly in large-scale genomic projects and resource-limited settings where sequencing at higher coverage could prove to be prohibitively expensive.

This evaluation refers to version 1 of the preprint

This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.127 ), and has published the reviews under the same license. For a video summary from the author see: https://youtu.be/x6oVzt_H_Pk?si=Byufhl0mIL3h0K6u

The reviews are as follows:

Reviewer 1. Jong Bhak:

Severe cases of covid-19 patients are critical data. This manuscript deals with detailed clinical information genome set as a subset of exome sequences and provide invaluable data for on-going global covid-19 omics studies.

Reviewer 2. Alfredo Iacoangeli:

The authors present the release of a new dataset that include low coverage WGS data of 79 individuals who experienced severe covid-19 in Madrid (Spain). The authors processed the data and imputed common variants and they are making this dataset available to the scientific community. They also present the clinical data of these patients in a descriptive and informative fashion. Finally, the authors also validated the quantify of their imputation, showcasing the potential of low coverage WGS as an alternative to microarrays. Overall the manuscript is written very well, clear, and exhaustive. The data is certainly valuable. Its generation and processing and analysis appears robust.

Overall I support the publication of this article and dataset. I only have a small number of minor suggestions for the authors: The sentence "Traditionally, the genotyping process has relied on array technologies as the standard, both at the broader GWAS level and the more specific genetic scoring and genetic diagnostics levels" sounds a little off. I totally understand where the authors come from but given the central role of NGS and Sanger for genetic diagnostics I would suggest the authors to modify accordingly or to keep the GWAS focus.

Please double-check the use a statistical terms in the description of the imputed data. For example: "On average, each VCF file in this rich dataset contains 9.49 million high-confidence single nucleotide variants [95%CI: 9.37 million - 9.61 million] (Figure 1)." The use of CI in this context is a little miss-leading as it is not strictly referring to a distribution of probability but to a finite collection. A range would be more appropriate. The authors say that they examined the ethnicity of the 79 individuals, however I do not think the ancestry is actually reported anywhere while a few figures show ancestral population data. The authors might clarify or correct the terminology.

Looking at figure 2 the sentence " although the male age distribution exhibits a broader range and higher variability, suggestive of a greater" does not appear justified. The authors might want to clarify or correct accordingly.

The sentence "This exploratory analysis highlights the diverse ways in which severe COVID-19 can present, and the importance of comprehensive and nuanced clinical phenotyping in improving our understanding and management of the disease." suggests some basic clustering might be useful. The readers might benefit from a couple of graphs or figures quantifying the overlap of the SNPs across samples and maybe one that shows the density of SNPs across the genome.

https://www.youtube.com/watch?v=VZCT4xwimvU

https://www.reddit.com/r/Wikipediavideos/

https://www.youtube.com/watch?v=3PLhzIaPamc

https://www.reddit.com/r/Wikipediavideos/

Is eq. 25 only used for teleop and eq. 24 used for normal (autonomous) operation?

This would help think through a Wardley Map for a product.