diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index dda4261..2172294 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,18 +1,13 @@ ## Description -These changes PURPOSE, because REASON. +These PR PURPOSE, because REASON. Closes # -## Reviewer Focus - This PR needs a quick/in-depth review. -Focus on CHANGES. - ## Checklist -- [ ] Ran spell-check - [ ] Formatted Markdown -- [ ] Rendered website locally +- [ ] Ran `just run-all` diff --git a/LICENSE.md b/LICENSE.md index 0fb847e..6d8cd69 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -33,7 +33,7 @@ exhaustive, and do not form part of our licenses. material not subject to the license. This includes other CC- licensed material, or material used under an exception or limitation to copyright. More considerations for licensors: - wiki.creativecommons.org/Considerations_for_licensors + wiki.creativecommons.org/Considerations_for_licensors Considerations for the public: By using one of our public licenses, a licensor grants the public permission to use the @@ -49,8 +49,8 @@ exhaustive, and do not form part of our licenses. such as asking that all changes be marked or described. Although not required by our licenses, you are encouraged to respect those requests where reasonable. More considerations - for the public: - wiki.creativecommons.org/Considerations_for_licensees + for the public: + wiki.creativecommons.org/Considerations_for_licensees ======================================================================= @@ -65,7 +65,6 @@ these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions. - Section 1 -- Definitions. a. Adapted Material means material subject to Copyright and Similar @@ -129,7 +128,6 @@ Section 1 -- Definitions. k. You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning. - Section 2 -- Scope. a. License grant. @@ -206,7 +204,6 @@ Section 2 -- Scope. licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties. - Section 3 -- License Conditions. Your exercise of the Licensed Rights is expressly made subject to the @@ -258,7 +255,6 @@ following conditions. License You apply must not prevent recipients of the Adapted Material from complying with this Public License. - Section 4 -- Sui Generis Database Rights. Where the Licensed Rights include Sui Generis Database Rights that @@ -280,7 +276,6 @@ For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights. - Section 5 -- Disclaimer of Warranties and Limitation of Liability. a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE @@ -309,7 +304,6 @@ Section 5 -- Disclaimer of Warranties and Limitation of Liability. possible, most closely approximates an absolute disclaimer and waiver of all liability. - Section 6 -- Term and Termination. a. This Public License applies for the term of the Copyright and @@ -338,7 +332,6 @@ Section 6 -- Term and Termination. d. Sections 1, 5, 6, 7, and 8 survive termination of this Public License. - Section 7 -- Other Terms and Conditions. a. The Licensor shall not be bound by any additional or different @@ -348,7 +341,6 @@ Section 7 -- Other Terms and Conditions. Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License. - Section 8 -- Interpretation. a. For the avoidance of doubt, this Public License does not, and @@ -372,7 +364,6 @@ Section 8 -- Interpretation. that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority. - ======================================================================= Creative Commons is not a party to its public diff --git a/_quarto.yml b/_quarto.yml index e0206a7..176932a 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -8,14 +8,17 @@ website: page-navigation: true body-header: | ::: {.callout-warning appearance="default" icon="true"} - 🚧 Sprout is still in active development and evolving quickly, so the - documentation and functionality may not work as described - and could undergo substantial changes 🚧 + 🚧 This website and documentation is still in very active development and + evolving quickly, so content could undergo substantial changes at any time + 🚧 ::: navbar: pinned: true left: - index.qmd + - motivation.qmd + - strategy.qmd + - groups.qmd tools: - icon: github href: "https://github.com/dp-next/wp1-ros" @@ -23,19 +26,8 @@ website: - icon: house href: https://dp-next.github.io aria-label: "House icon: DP-Next home page" - sidebar: - - id: wp1 - style: "floating" - collapse-level: 2 - contents: - - wp1/index.qmd - - wp1/introduction.qmd - - wp1/strategy.qmd - - wp1/roadmap.qmd - - wp1/application.qmd -format: - html +format: html bibliography: references.bib csl: vancouver.csl diff --git a/abstract.qmd b/abstract.qmd deleted file mode 100644 index f25e853..0000000 --- a/abstract.qmd +++ /dev/null @@ -1,43 +0,0 @@ ---- -title: "Abstract" -description: "Doing 'better research in less time' by following modern collaboration, open, and planning practices." ---- - -Science, while generating cutting-edge knowledge, lags behind most -industry settings when it comes to practical, operational aspects. For -instance, while much of research done now relies heavily on software and -computational work, funding agencies rarely fund software and data -engineering projects, nor do many research groups hire these highly -skilled technical personnel. So, the aim of Work Package 1 is to -establish these skills and needs as a core component of this project and -to help do "better research in less time". - -Our basic strategies will be to establish working groups, including a -group dedicated to "research operations" to fulfil this core aim, as -well as developing and implementing common practices and tools that -maximise collaboration and that follow some guiding principles. All -groups will include a "tech lead" who has technical knowledge and skills -and who will also be part of the research operations group, to help -coordinate WP groups with these practices. We aim to onboard and train -the tech leads in these practices by embedding them in some work done at -SDCA, where these practices have been developing and refining over the -last several years. The most relevant practices and skills that this WP1 -aims to provide are in software and data engineering, iterative project -management, collaborative workflows and tools, - -Pertinent to these practices is understanding and assessing risk and -challenges. The two biggest challenges we face with this WP1 are: - -1. The need for highly technical personnel who have sufficient - fundamental expertise to understand and apply these practices, which - we hope to minimise through the training and onboarding of the tech - leads. -2. the IT systems across centers that often don’t work well together, - which we hope to reduce the impact of by having a dedicated research - operations group. - -While this WP1 forms the foundation to all other WPs and in many ways -aims to support their success, the activities of WP1 are an increasingly -needed aspect of research globally. In this regard, we aim to produce -tangible and usable deliverables that are independent and valuable on -their own. diff --git a/application.qmd b/application.qmd deleted file mode 100644 index 75529f6..0000000 --- a/application.qmd +++ /dev/null @@ -1,91 +0,0 @@ ---- -title: "Applications" -description: Content used for the first and second rounds of applications. ---- - -## First round - -- **Characters**: 644 - -WP1 answers the increasing need for openness, transparency, and -reproducibility in research, will deliver the day-to-day project and -operations management of all the WPs and will facilitate close -collaboration and joint expertise development across all Steno Centres. - -Effective coordination and management of complex projects such as -DP-Next requires modern and innovative approaches to project and -operational management. We will employ tools developed and tested at -SDCA in the past years [@Johnston2022; @DARTER; @ukbaid; @seedcase; -@sdca-github] to offer a practical framework for sharing knowledge and -technical skills across centres, aiming to deliver "better research done -in less time" [@Lowndes2017]. - -## Second round - -- **Characters**: 2200 / 1800 characters - -Science, while pursuing cutting edge knowledge, lags behind industry in -standard operational, organisational, and technological practices, -tools, and methods. From this, the core visions of WP1 are to do better -research in less time [@Lowndes2017] and expand the capacity of modern -technical engineering-based skills in research groups across Steno and -Denmark. By applying modern operational, engineering, and project -management practices, we will optimize work done across the WPs. Through -formal and informal upskilling sessions, we will develop data -engineering and modern collaborative skills and knowledge in researchers -from across the Steno Centers. - -At SDCA, we have been developing and applying these practices in -multiple projects [@Johnston2022; @DARTER; @ukbaid; @seedcase; -@sdca-github], which highlight tangible examples of WP1's activities. -The general strategy for WP1 is to: 1) develop and agree on some basic -principles for collaboration between centers and WPs that adhere to open -scientific practices and modern collaborative methods; 2) investigate -potential barriers to effective cross-Steno collaboration; 3) decide on -a set of common tools and standards to use across centers for WP. -Specific actions and tasks are found in @fig-gantt-wp1 and @fig-actions. - -Aside from the traditional management group overseeing the project, we -will also have a research operations group that will simplify, -streamline, and automate the collaboration and coordination of -activities and products between WPs and centers as well as provide a -space for learning these technical skills. See @fig-organization and the -collaboration section below for more details, as well as @fig-gantt for -the general project timeline. - -A major component of WP1 is also upskilling activities, in collaboration -with the NNF-funded software and training-based Seedcase Project -[@seedcase]. Training will focus on skills not often taught to -researchers, such as data engineering, modern collaborative practices, -and iterative project management methods. - -More detail on this WP can be found on the DP-Next website -(https://steno-aarhus.github.io/dp-next/wp1/), such as the roadmap, -potential challenges, and strategy. - -::: column-page -::: {#fig-app-round2 layout-ncol="2"} -```{mermaid} -%%| file: images/gantt.mmd -%%| fig-width: 7 -%%| label: fig-gantt -%%| fig-cap: "General Gantt chart for all of DP-Next." -``` - -```{mermaid} -%%| file: images/gantt-wp1.mmd -%%| label: fig-gantt-wp1 -%%| fig-cap: "Gantt chart for Work Package 1" -``` - -![Groups and people working on -DP-Next.](images/organization.svg){#fig-organization} - -![Actions and task for WP1.](images/actions.svg){#fig-actions} - -Project planning, organization, and operational actions faciliated by -WP1. -::: -::: - -## References diff --git a/decisions/_template.qmd b/decisions/_template.qmd new file mode 100644 index 0000000..cf21ee0 --- /dev/null +++ b/decisions/_template.qmd @@ -0,0 +1,66 @@ +--- +title: "" +description: "Our reasons for ..." +date: "" +categories: +--- + +::: content-hidden +Use other decision posts as inspiration to writing these. +Leave the content-hidden sections in the text for future reference. +::: + +## Context and problem statement + +::: content-hidden +State the context and some background on the issue, then write a +statement in the form of a question for the problem. +::: + +## Decision drivers + +::: content-hidden +List some reasons for why we need to make this decision and what things +have arisen that impact work. +::: + +## Considered options + +::: content-hidden +List and describe some of the options, as well as some of the benefits and +drawbacks for each option. +::: + +### Option 1 + +::: {.columns} +::: {.column} +#### Benefits + +- Item 1 +::: +::: {.column} +#### Drawbacks + +- Item 1 +::: +::: + +## Decision outcome + +::: content-hidden +What decision was made, use the form "We decided on CHOICE because of +REASONS." +::: + +### Consequences + +::: content-hidden +List some potential consequences of this decision. +::: + +## Resources used for this post + +::: content-hidden +List the resources used to write this post +::: diff --git a/groups.qmd b/groups.qmd new file mode 100644 index 0000000..e730034 --- /dev/null +++ b/groups.qmd @@ -0,0 +1,25 @@ +--- +title: "Groups" +toc: false +--- + +![Groups and people working on DP-Next.](images/organization.svg) + +### Management group + +The project will be led by the principal investigator, with support from +the co-applicants / Work Package leaders, who together form the +management group. This group will be responsible for the overall +coordination of the project and ensuring it's successful completion. + +### Technical working group + +The technical working group will be responsible for the more technical +and practical aspects of the project, primarily being responsible for +fulfilling the aims of Work Package 1. This group will, at a minimum, be +composed of at least one person from each work package (and preferably +in each Steno center to support our upskilling aims) who acts as a "tech +lead" for that work package. This group will keep track of some +day-to-day operations ("research operations"), identify ways to reduce +technical barriers, improve on and support effective collaborative +practices, as well as ensuring the research is reproducible and open. diff --git a/images/gantt-wp1.mmd b/images/gantt-wp1.mmd index 9618da2..ee2ac14 100644 --- a/images/gantt-wp1.mmd +++ b/images/gantt-wp1.mmd @@ -1,5 +1,5 @@ %%{init: { - 'theme': 'neutral', + 'theme': 'neutral', 'gantt': { 'barHeight': 25, 'leftPadding': 100 @@ -14,13 +14,13 @@ gantt %% (`excludes` accepts specific dates in YYYY-MM-DD format, days of the week ("sunday") or "weekends", but not the word "weekdays".) section Ongoing
activities - T4. Iterate and refine collaboration: imp_collab, 2025-01-01, 5y + T4. Iterate and refine collaboration: imp_collab, 2025-09-01, 5y T5. Develop project website: imp_proj_web, after collab_agree, 2030-01-01 T9. Develop research ops website: imp_reops_web, after consensus, 2030-01-01 T10. Maintain data infrastructure: imp_seedcase, after seedcase, 2030-01-01 section General
setup - T1. Establish working groups: wg, 2025-01-01, 2M + T1. Establish working groups: wg, 2025-09-01, 2M T2. Decide on collaboration approaches: collab_agree, after wg, 10M T3. Identify collaboration barriers: barriers, after wg, 10M M1. Setup project website: milestone, web_proj, after barriers, 1M @@ -34,12 +34,12 @@ gantt section WP3-linked
activities T7. Setup data engineering pipeline: de_wp3, after web_proj, 6M D2. Data engineering pipeline report: milestone, der_wp3, after de_wp3, 1M - D3. Data Management Plan template: milestone, template_dmp, 2027-01-01, 1M + D3. Data Management Plan template: milestone, template_dmp, 2027-01-01, 1M M4. Setup data infrastructure: milestone, seedcase, 2027-01-01, 1M section WP4-linked
activities M2. Setup knowledge repo: milestone, kr_wp4, after collab_agree, 1M - T8. Build knowledge dissemination pipeline: kmp_wp4, after kr_wp4, 6M + T8. Build knowledge dissemination pipeline: kmp_wp4, after kr_wp4, 6M diff --git a/images/gantt.mmd b/images/gantt.mmd index 3eaf0d5..d479b8a 100644 --- a/images/gantt.mmd +++ b/images/gantt.mmd @@ -1,5 +1,5 @@ %%{init: { - 'theme': 'neutral', + 'theme': 'neutral', 'gantt': { 'barHeight': 25, 'leftPadding': 125 @@ -14,11 +14,11 @@ gantt %% (`excludes` accepts specific dates in YYYY-MM-DD format, days of the week ("sunday") or "weekends", but not the word "weekdays".) section WP1
Management
and Collaboration - T1.1 General project management: t1_1, 2025-01-01, 5y - T1.2 Optimising collaboration: t1_2, 2025-01-01, 5y + T1.1 General project management: t1_1, 2025-09-01, 5y + T1.2 Optimising collaboration: t1_2, 2025-09-01, 5y section WP2
Risk Prediction - T2.1 Separate model development: t2_1, 2025-01-01, 18M + T2.1 Separate model development: t2_1, 2025-09-01, 18M T2.2 Machine Learning approaches: t2_2, 2026-01-01, 18M T2.3 Joint model development: t2_3, 2026-07-01, 18M T2.4 Validation: t2_4, 2028-01-01, 18M @@ -28,7 +28,7 @@ gantt T3.2 Deep phenotyping substudy: t3_2, 2025-07-01, 54M section WP4
Development
and intervention - T4.1 Investigate barriers and facilitators: t4_1, 2025-01-01, 18M + T4.1 Investigate barriers and facilitators: t4_1, 2025-09-01, 18M T4.2 Develop & co-design: t4_2, after t4_1, 18M T4.3 Pilot test in specific populations: t4_3, after t4_2, 1y T4.4 Evaluation: t4_4, 2028-07-01, 18M diff --git a/index.qmd b/index.qmd new file mode 100644 index 0000000..8c3d227 --- /dev/null +++ b/index.qmd @@ -0,0 +1,89 @@ +--- +title: "Better research in less time and fewer resources" +toc: false +--- + +::: column-page +## Visions + +- Better, reproducible, and open research done in less time and + with fewer resources + +- Researchers with modern technical engineering-based and project + management skills embedded in more research groups + +- Modern data engineering practices and research operational + approaches established as a standard of practice when conducting + research + +## Strategies + +- Create management groups to manage and coordinate centers and work + packages in completing their deliverables. + +- Develop and implement cross-Steno *Research Operations* and modern + collaborative workflows and practices that support the successful + completion of each work package as well as improving research + practices across Steno centers. + +- Optimise and reduce the time and effort spent between designing the + work package studies and the final dissemination of high-quality + research results. + +- Incorporate reproducible and open science practices into the + research workflow to both improve the quality of research and reduce + the time spent on data processing, analysis, and dissemination. + +- Build up inter- and intra-Steno knowledge and skill capacity + ("upskill") in non-traditional technical skills and knowledge such + as software development, data engineering, operational management + (including "DataOps"), and iterative project management practices. +::: + +## Sciences lags behind in many practical and technical aspects + +Science, while generating cutting-edge knowledge, lags behind most +industry settings when it comes to practical, operational aspects. For +example, while much of research done now relies heavily on software and +computational work, funding agencies rarely fund software and data +engineering projects, nor do many research groups hire these highly +skilled technical personnel. + +We hope, through Work Package 1, to establish these skills and needs as +a core component of the DP-Next project and to help do "better research +in less time". + +## A core strategy is to establish a "technical" working group + +By having a dedicated working group that works to fulfil the aims of +this work package, we hope to emphasize the importance of these +practices and to ensure they are implemented across all work packages. +All groups will include a "tech lead" who has technical knowledge and +skills and who will be a part of this technical working group, to help +coordinate work package groups with these practices. + +We aim to onboard and train the tech leads in these practices by +embedding them in some work done at SDCA, where these practices have +been developing and refining over the last several years. + +## Plenty of risks and challenges + +The two biggest challenges we face with Work Package 1 are: + +1. The need for highly technical personnel who have sufficient + fundamental expertise to understand and apply these practices, which + we hope to minimise through the training and onboarding of the tech + leads. +2. The IT systems across centers that often don’t work well together, + which we hope to reduce the impact of by having a dedicated research + operations group. + +## We aren't just support, we are a core component of research + +While Work Package 1 forms the foundation to all work packages of +DP-Next, and in many ways aims to support their success, our activities +are an increasingly needed aspect of research throughout the world. + +So, aside from completing the responsibilities and tasks we have for +DP-Next, we also aim to produce tangible and usable deliverables that +are independent and valuable on their own. diff --git a/introduction.qmd b/introduction.qmd deleted file mode 100644 index 7f4a68d..0000000 --- a/introduction.qmd +++ /dev/null @@ -1,79 +0,0 @@ ---- -title: "Introduction" -description: Background and motivation for project as well as its visions and aims. ---- - -Science is state of the art in seeking and gaining knowledge, and yet it -lags far behind in general operational, organisational, and -technological aspects when compared to industry settings. For instance, -there are nearly no research software engineers within research groups -or institutions, even though software is a foundational component to -conducting research in the modern era. - -Likewise, basic modern communication and project management tools are -rarely, if ever, used within research environments, even though they are -standard practice in many corporate settings. If these things are used -by some groups, they are not shared nor advertised through traditional -scientific publications, so if they exist, others can't reuse and learn -from each other to improve how we do research. - -Science is also increasingly moving into more team-based, multi-centered -enterprises, as well as having a greater requirement for openness and -reproducibility. These require using modern practices designed for these -conditions, rarely seen in academia but common within many industry -settings. - -Our aim with WP1 is to deliver "better, open, and reproducible research -done in less time" by employing these practices, as well as providing -upskilling opportunities to researchers for skills and knowledge in -these practices. - -We’ve structured and organised Work Package 1 (WP1) based on the -increasing need for openness, transparency, and reproducibility in -research. WP1 will deliver the day-to-day project and operations -management of all the WPs, as well as facilitating the close -collaboration and joint development of expertise across all seven Steno -Centers. - -To achieve effective and optimal coordination and management of -a complex project like this, we will apply modern and innovative methods -in project and operational management practices, as well as applying a -software and data engineering structure and perspective both operational -aspects as well as to scientific outputs. We will employ resources and -tools developed and tested at SDCA in the past years [@Johnston2022; -@DARTER; @ukbaid; @seedcase; @sdca-github] to offer a practical -framework for sharing knowledge and technical skills across centres, -which will deliver "better research done in less time" [@Lowndes2017] -while following reproducible and open scientific practices. - -## Visions - -- *Better research done in less time* - -- *Researchers with modern technical engineering-based and project - management skills embedded in more groups* - -- *Modern data engineering practices and research operational - approaches established as a standard of practice when conducting - research* - -## Aims - -- Create management groups to manage and coordinate centers and WPs in - completing their deliverables. - -- Develop and implement cross-Steno Research Operations and modern - collaborative workflows and practices that support the successful - completion of each work package as well as improving research - practices across Steno centers. - -- Optimise and reduce the time and effort spent between designing the - work package studies and the final disseminating high-quality - research results. - -- Build up inter- and intra-Steno knowledge and skill capacity - ("upskill") in non-traditional technical skills and knowledge such - as software development, data engineering, operational management - (including "DataOps"), and iterative project management practices. - -## References diff --git a/justfile b/justfile index 0a35eb2..c0f7c1d 100644 --- a/justfile +++ b/justfile @@ -1,10 +1,13 @@ @_default: just --list --unsorted +# Run all recipes +run-all: build-website + # Generate PNG images from PlantUML files generate-puml: docker run --rm -v $(pwd):/puml -w /puml ghcr.io/plantuml/plantuml:latest -tsvg "**/*.puml" # Build the website using Quarto build-website: - quarto preview + quarto render diff --git a/motivation.qmd b/motivation.qmd new file mode 100644 index 0000000..16a05d2 --- /dev/null +++ b/motivation.qmd @@ -0,0 +1,43 @@ +--- +title: "Motivation" +description: Background and motivation for Work Package 1. +toc: false +--- + +## Academia lags far behind industry in many practical ways + +Science, while pursuing cutting edge knowledge, lags far behind industry +in standard operational, organisational, and technological practices, +tools, and methods. For example, there are nearly no research software +or data engineers within research groups or institutions, even though +software and data are foundational components to conducting research in +the modern era. + +Traditional management of larger scale research projects often involves +setting up steering committees who check on progress through status +updates and discuss solutions to issues that arise. However, there are +many modern tools and methods used within industry that research +environments and projects could benefit from, such as data engineering, +software development, and operations management. + +Likewise, basic modern communication and project management tools are +rarely, if ever, used within research environments, even though they are +standard practice in many corporate settings. If these things are used +by some groups, they are not shared nor advertised through traditional +scientific publications, so if they exist, others can't reuse and learn +from each other to improve how we do research. + +## Science needs more team-based, collaborative approaches + +Science is also increasingly moving into more team-based, multi-centered +enterprises, as well as having a greater requirement for openness and +reproducibility. These require using modern practices designed for these +conditions, rarely seen in academia but common within many industry +settings. + +Ultimately, academia needs to recognize and incorporate these practices +in order to stay relevant and competitive in the modern research +landscape. But we need more funds, support, awareness, and training to +make this happen. + +This is what Work Package 1 aims to help address. diff --git a/strategy.qmd b/strategy.qmd index 843dea8..b4913c5 100644 --- a/strategy.qmd +++ b/strategy.qmd @@ -1,30 +1,22 @@ --- title: "Strategy" -description: Strategic principles and practical details for WP1. +description: Strategic principles and actions taken in Work Package 1. --- -Traditional management of larger scale research projects often involves -setting up steering committees who check on progress through status -updates and discuss solutions to issues that arise. However, there are -many modern tools and methods used within industry that research -environments and projects could benefit from, such as data engineering, -software development, and operations management. Thus, our general -strategy incorporates not only the standard project management -activities as well as modern approaches to coordinating tasks and -outputs between groups. The general strategies we’ll take are to: - -- Establish an overall management group and a research operations - group of relevant persons from each center to track progress, - coordinate tasks, and manage the project. -- Develop and agree on some guiding principles for collaboration and - work to follow across centers and WPs that adhere to open science - practices. -- Investigate and identify resources, limitations, and barriers on - cross-Steno collaboration practices and processes. -- Develop and agree on a set of common tools and standards to use - across centers for WP to have smoother collaboration and sharing of - outputs, that also consider the barriers and resources as well as - the guiding principles. +We've structured and organised Work Package 1 based on the +increasing need for openness, transparency, and reproducibility in +research. Work Package 1 will deliver the day-to-day project and operations +management of all the work packages, as well as facilitating the close +collaboration and joint development of expertise across all seven Steno +Centers. + +To achieve effective and optimal coordination and management of +a complex project like this, we will employ resources and +tools developed and tested at the Steno Diabetes Center Aarhus in the past years [@Johnston2022; +@DARTER; @ukbaid; @seedcase; @sdca-github] to offer a practical +framework for sharing knowledge and technical skills across centres, +which will deliver "better research done in less time" [@Lowndes2017] +while following reproducible and open scientific practices. ## Guiding principles @@ -32,7 +24,7 @@ One of the initial steps in the strategy involves developing and implementing general principles that will guide collaboration and work across the Steno Centers. This ensures we have a basis for following a common approach to working and communicating together when managing the -WPs. While we will finalise and refine the principles during the first +work packages. While we will finalise and refine the principles during the first year of the project, below are some principles that will form the basis for all other principles. @@ -47,9 +39,102 @@ for all other principles. processing/management using code-based and programmatic pipeline/workflow management +## Specifics of the strategy + +Expanding on the strategies listed on the [landing page](index.qmd), +the below describes more of the details about the specific strategies from a technical or digital perspective. +Specific actions and tasks are found in a later section, as well as in @fig-actions. + +### Project management + +While general project management and coordination will be done by the +management [group](groups.qmd), the technical strategy for the project +management will involve applying iterative and incremental methods +often used in software development, such as Agile-inspired methods. In +particular, this involves using a (digital) board to track tasks and +using regular "reflection" meetings to identify things that work +and things to improve on in our collaboration and management. The +Seedcase Project team at Steno Aarhus uses these practices with +very good results. + +### Collaborative practices + +Building an effective collaboration between groups, centers, and people +requires agreeing to a set of common practices that we all adhere to. +In this way, we'll develop a description of basic standards and practices +that we will discuss, refine, and agree on during the first year of the project. +These documents will be living documents that we will post publicly on +this website. + +## Research operations + +The aim of research operations is to optimise day-to-day work in order +to minimise time and effort spent per unit of output. + +we will apply modern and innovative methods +in project and operational management practices, + + +Investigate and identify resources, limitations, and barriers on +cross-Steno collaboration practices and processes. +root + +## Software development + +will simplify, +streamline, and automate the collaboration and coordination of +activities and products between WPs and centers as well as provide a +space for learning these technical skills. + +- Regularly seek to identify and implement ways to simplify, streamline, +and automate activities throughout the research life cycle of DP-Next and +the other Work Packages. + +## Data engineering + +## Technical working group + +- Establish an overall management group and a research operations + group of relevant persons from each center to track progress, + coordinate tasks, and manage the project. + + +## Upskilling + +A major component of WP1 is also upskilling activities, in collaboration +with the NNF-funded software and training-based Seedcase Project +[@seedcase]. Training will focus on skills not often taught to +researchers, such as data engineering, modern collaborative practices, +and iterative project management methods. + +Through +formal and informal upskilling sessions, we will develop data +engineering and modern collaborative skills and knowledge in researchers +from across the Steno Centers. + ## Actions -![Actions and task for WP1.](images/actions.svg) +Some of +the initial tasks revolve around establishing: + +- A communications channel +for everyone (as well as sub-channels for individual WPs and groups) +that make it easy to keep everyone updated and to view all +communications done (not emails). +- A project management platform visible +and usable by everyone. +- An effective project management approach that +groups can use to track tasks and deliverables (e.g. a suitable approach +might be using Kanban principles) +- A document sharing platform, +ensuring that all of these also follow the guiding principles. + +Later +tasks include developing the deliverables of the WPs in a way that makes +sharing and interoperability easier, both internal to the project groups +and WPs as well as to external stakeholders. + +![Actions and task for Work Package 1.](images/actions.svg){#fig-actions} ## Potential tools and methods to use @@ -58,24 +143,26 @@ decided upon by everyone. However, some of the tools and methods that we are considering that follow the principles include: - R for programming, data processing, and analysis -- GitHub to use as the knowledge repository +- GitHub to use as the knowledge and document repository - Quarto (next generation of R Markdown) for writing and sharing documents, as well as creating websites -- Slack/Teams/Discord for central communication +- Discord for central communication +- Teamup for central calendar and scheduling +- Agile-inspired iterative and incremental methods for project management - GitHub Projects for project management -- Agile (e.g. Scrum and Kanban) inspired iterative and incremental - methods for project management -- Seedcase software for data management and sharing +- Seedcase software for data infrastructure, management and sharing ## Potential barriers and challenges Aside from the standard project management tasks, implementing modern research ops and collaborative practices that support conducting open and reproducible science across all Steno Centers will be a challenge. -Given that personnel in research environments with the necessary -technical knowledge and skills are few and often move out of academia +Given that there are few personnel in research environments with the necessary +technical knowledge and skills and they often move out of academia into industry positions, a substantial amount of time and effort will be -spent in training and upskilling existing personnel. The reason we’ve +spent in training and upskilling existing personnel. + +The reason we’ve structured the groups to include at least one “tech lead” who is also part of the research ops group is to help minimise this challenge. We aim to provide training to this tech lead by embedding them in some of @@ -84,40 +171,8 @@ many of these practices. Another major challenge will be coordinating tasks and work between IT systems that often don’t work well together or are suboptimally designed -for cross-institution collaboration. This is one reason we’ve decided to -establish a research ops group, so that we can minimise the impact these +for cross-institution collaboration. This is one reason we've decided to +establish the technical working group, so that we can minimise the impact these issues have on completing the project deliverables. -## People and groups - -![Groups and people working on DP-Next.](images/organization.svg) - -### Management group - -The project will be led by the PI, with support from the co-applicants / -Work Package leaders, who together form the management group. Aside from -individual groups for each WP, there will also be a group dedicated to -overseeing the research operations. This group will, at a minimum, be -composed of at least one person from each WP (and preferably in each -center) who acts as a “tech lead” for that WP group. The tech lead -should be someone with above average literacy in -programming/computing/IT. - -### Research operations - -The aim of research operations is to optimise day-to-day work in order -to minimise time and effort spent per unit of output. The research ops -group will act as a unit that works to reduce tech barriers, develop -software and data engineering processes and tools, and advise on how to -best design the outputs of WPs that are the inputs of other WPs. Some of -the initial tasks revolve around establishing: a communications channel -for everyone (as well as sub-channels for individual WPs and groups) -that make it easy to keep everyone updated and to view all -communications done (not emails); a project management platform visible -and usable by everyone; an effective project management approach that -groups can use to track tasks and deliverables (e.g. a suitable approach -might be using Kanban principles); and a document sharing platform, -ensuring that all of these also follow the guiding principles. Later -tasks include developing the deliverables of the WPs in a way that makes -sharing and interoperability easier, both internal to the project groups -and WPs as well as to external stakeholders. +## References