diff --git a/_freeze/posts/2023-07-20_cross_company_dev/index/execute-results/html.json b/_freeze/posts/2023-07-20_cross_company_dev/index/execute-results/html.json deleted file mode 100644 index 8fee9923..00000000 --- a/_freeze/posts/2023-07-20_cross_company_dev/index/execute-results/html.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "hash": "31a77b8106e2a20bc0d23cd71a83e1fe", - "result": { - "markdown": "---\ntitle: \"Collaborative Open Source Development: Revolutionizing Data Standards in the Pharmaceutical Industry\"\nauthor:\n - name: Stefan Thoma\ndescription: \"\"\ndate: \"2023-07-20\"\ncategories: [WIP, admiral]\nimage: \"shiny_klee.png\"\neditor: \n markdown: \n wrap: sentence\n---\n\n\n\n\n\n\n\n\n\n\n\n# Introduction:\n\nIn the fast-paced world of pharmaceutical research and development, the need for efficient and standardized data management solutions has never been more crucial. \nThis blog post delves into the journey of an ambitious team working towards an end-to-end solution in R, particularly focusing on the transformation from SDTM to ADaM, while advocating for collaborative open-source development across companies. \nWe will explore the challenges we faced, the strategies we employed, and the significant impact this approach has had on both Roche and the industry as a whole.\n\n## Who am I:\nI joined Roche as an intern in November 2022, and since April, I have become a permanent member of the Admiral team, dedicating 20% of my time to this project.\n\n# Problem to be solved:\nThe lack of a comprehensive, standardized solution in R for end-to-end clinical data analysis presented a significant challenge in the industry. Many companies developed their own custom solutions, resulting in a fragmented landscape. Even individuals proficient in SAS had to relearn company-specific solutions, leading to inefficiencies and delays. The team recognized the need for an end-to-end framework. The admiral package covers the transformation from SDTM to ADaM, addressing a specific part of this pipeline.\n\n# Proposed Solution:\nEnter Admiral! Admiral is not a Roche product, but a collaborative effort that aims to create an open-source package to solve the data standards challenge. The vision was to develop a solution that would be widely accessible, fostering collaboration and standardization across the pharmaceutical industry.\n\n# Challenges at Startup:\nLaunching a collaborative open-source project is no small feat. The team faced the task of convincing higher-ups and peers about the value and relevance of the project. By demonstrating the real problem that needed solving, they managed to gain support from key stakeholders. Furthermore, they sought to expand their influence beyond Roche and reached out to other companies, forming a team consisting of Thomas Neitmann from Roche and Marco Rimmler from GSK, right from the start.\n\n# Strategies:\nTo ensure success, the team adopted several key strategies. Acting quickly was imperative, as they open-sourced the project at an early stage and communicated their intentions widely. By involving multiple companies, they fostered a collaborative community, where users could actively participate in the development process, providing feedback and creating issues. The team also embraced a modular approach, developing a core package alongside therapeutic area-specific packages and internal company packages. This modularity was complemented by consistent interfaces and design guidelines across all packages, facilitated by a developer's guide and continuous integration and continuous deployment (CICD). Furthermore, they created templates for common and more complex tasks, enhancing productivity and efficiency.\n\n# Impact for Roche:\nFor Roche, the adoption of the Admiral project yielded remarkable benefits. Instead of relying on just two developers, they gained the power of a full team consisting of ten developers. This amplified workforce not only accelerated progress but also provided Roche with a seat at the table. By collaborating with other companies, Roche ensured that they were part of the conversation, driving industry-wide standards.\n\n# Attractive Workplace:\nEmbracing open-source development and utilizing R as a primary tool for data management also made Roche an attractive workplace for talented individuals. Open-source development inherently promotes transparency and ethics, appealing to those seeking a more collaborative and inclusive work environment. The collaboration across companies dissolved traditional hierarchies, encouraging autonomous work and empowering individuals to choose the issues they wished to tackle. Additionally, this approach expanded networks and facilitated knowledge transfer, making talent more adaptable and valuable across various positions.\n\n# Conclusion:\nThe benefits of developing open-source packages across companies, as exemplified by the Admiral project, are truly transformative. By pooling resources, knowledge, and expertise, companies in the pharmaceutical industry can overcome the challenges of data management and foster a culture of collaboration and standardization. The impact extends beyond immediate gains in efficiency and productivity; it attracts new hires, encourages transparency, and cultivates a vibrant community of professionals dedicated to advancing pharmaceutical research and development. The Admiral project serves as a testament to the power of collaborative open-source development and the potential it holds for the future of the industry.\n\n\n\n\n::: {.cell}\n\n:::\n", - "supporting": [], - "filters": [ - "rmarkdown/pagebreak.lua" - ], - "includes": {}, - "engineDependencies": {}, - "preserve": {}, - "postProcess": true - } -} \ No newline at end of file diff --git a/posts/2023-07-20_cross_company_dev/cross_industry_dev.qmd b/posts/2023-07-20_cross_company_dev/cross_industry_dev.qmd index 92f8e09c..6ccd25ed 100644 --- a/posts/2023-07-20_cross_company_dev/cross_industry_dev.qmd +++ b/posts/2023-07-20_cross_company_dev/cross_industry_dev.qmd @@ -40,9 +40,9 @@ As the industry moves toward new (to them) programming languages, fit-for-purpos The realization that siloed solutions -- in an area where competitiveness does not benefit patients -- are simply resource hungry ways to solve the same problem in parallel provided a great argument for a shift toward collaborations. Such cross-industry collaborations gave rise to the pharmaverse, an opinionated collection of R packages designed to solve clinical reporting in R. -[{admiral}](https://github.com/pharmaverse/admiral), the project that I work on, is part of the pharmaverse and covers the creation of ADaM data sets (CDISC standard data). +[{admiral}](https://github.com/pharmaverse/admiral), the project that I work on, is part of the [pharmaverse](https://pharmaverse.github.io/admiraldev/devel/index.html) and covers the creation of ADaM data sets (CDISC standard data). These data sets are subsequently used to produce tables, listings, and graphs and are usually part of the submission package for regulators. -You can read about the inception of {admiral} in [this recent blog post by ...](). + @@ -51,31 +51,31 @@ You can read about the inception of {admiral} in [this recent blog post by ...]( When creating an open source package in an industry where currently there is a lot of traction you have to move fast. No, I don't mean: Move fast and break things. I mean: Communicate! Get people on board! -We aimed {admiral} to be **the** package for ADaM creation even before deciding to create the package together with GSK. +We aimed [{admiral}](https://github.com/pharmaverse/admiral) to be **the** package for ADaM creation even before deciding to create the package together with GSK. By being transparent about our endeavor, e.g. Thomas Neitmann (then at Roche) posting on LinkedIn, we managed to connect with Micheal Rimler from GSK and soon realized that we were dealing with the exact same challenge at both companies, and that a collaborative effort would improve the final product while reducing individual efforts. -A working prototype of {admiral} was to be created by GSK and Roche within six months, and would then be open sourced. -In our effort to communicate openly, we informed statistical programmers from over 20 companies about the {admiral} project and invited them to try it out and provide feedback once released. +A working prototype of [{admiral}](https://github.com/pharmaverse/admiral) was to be created by GSK and Roche within six months, and would then be open sourced. +In our effort to communicate openly, we informed statistical programmers from over 20 companies about the [{admiral}](https://github.com/pharmaverse/admiral) project and invited them to try it out and provide feedback once released. In the end, we received over 500 comments from over 50 programmers. This was instrumental in creating a product that was optimised for general usage in the clinical reporting field and ensured that other companies would not unknowingly invest into their own solution to this challenge. Open sourcing early is particularly beneficial because this ensures from the get-go that code created is aimed at a general audience, and not company specific (perhaps by accident). -{admiral} was created with the long term goal of having a stable and flexible solution for the clinical reporting pipeline. -In that spirit, its permissive apache 2.0 licence (jointly owned by Roche and GSK) further strengthens trust into the the project, namely for three reasons: +[{admiral}](https://github.com/pharmaverse/admiral) was created with the long term goal of having a stable and flexible solution for the clinical reporting pipeline. +In that spirit, its permissive [apache 2.0 licence](https://www.apache.org/licenses/LICENSE-2.0) (jointly owned by Roche and GSK) further strengthens trust into the the project, namely for three reasons: - Jointly owned means that efforts to monetize the code-base by one company could be vetoed by the other. The permissive licence ensures that in such an unlikely case, the code-base that has been published would stay available and could always be used and improved upon by others. - Having this package backed by Roche and GSK ensures (as far as this is ever possible) funding for properly maintaining the packages. This is crucial, as a package is rarely **finished**. -Up to now, experts from many more companies have joined {admiral} or one of its therapeutic area specific package-extensions, inspiring even more trust into its reliability. +Up to now, experts from many more companies have joined [{admiral}](https://github.com/pharmaverse/admiral) or one of its therapeutic area specific package-extensions, inspiring even more trust into its reliability. If you would like to learn more about licenses for open source projects in the clinical reporting world please check out the [recent E2E guidence on open source license](https://phuse-org.github.io/E2E-OS-Guidance/) ## Development workflow -Every improvement, task, or feature we want to implement on {admiral} starts as an issue on our [GitHub repository](https://github.com/pharmaverse/admiral). +Every improvement, task, or feature we want to implement on [{admiral}](https://github.com/pharmaverse/admiral) starts as an issue on our [GitHub repository](https://github.com/pharmaverse/admiral). It is the centerpiece of our development workflow, along with our [developer guides](https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html) which describe in detail the strategies, conventions, and workflows used in development. -The guides help us keep the {admiral} package internally consistent (e.g. naming conventions, function logic) but also ensure that {admiral} adjacent packages follow the same conventions and share the user interface. +The guides help us keep the [{admiral}](https://github.com/pharmaverse/admiral) package internally consistent (e.g. naming conventions, function logic) but also ensure that [{admiral}](https://github.com/pharmaverse/admiral) adjacent packages follow the same conventions and share the user interface. This is further helped by the implemented CICD pipeline which ensures styling convention and spelling (and much more). @@ -84,19 +84,20 @@ Here, the role of product lead (currently [Edoardo Mancini](https://www.linkedin These stand-up meetings are centered around the [project-board](https://github.com/orgs/pharmaverse/projects/12) which gives a complete overview of activities and progress. Issues are mostly self-assigned so developers can really chose what they want to work on. -By design, {admiral} is community built. +![GitHub project board](project_board.png) + +By design, [{admiral}](https://github.com/pharmaverse/admiral) is community built. Most developers working on the project are statistical programmers working on clinical reporting themselves. -As an open source project, community input is highly valued, and anyone using admiral is encouraged to submit issues or take on issues as part of the development team. +As an open source project, community input is highly valued, and anyone using [{admiral}](https://github.com/pharmaverse/admiral) is encouraged to submit issues or take on issues as part of the development team. We also do occasional events to bring the statistical programmers community and the developers closer together. -Just last February we organised the {admiral} hackathon which had up to 500 participants. - +Just last February we organised the [{admiral}](https://github.com/pharmaverse/admiral) hackathon which had up to 500 participants. ## Impact -For Roche, this agreement is great: They get access to a programm created by specialists and users from across the industry but paying only a fraction of the developmental costs. +For Roche, cross-industry package development work out in their favor: They get access to software created by specialists and users from across the industry but paying only a fraction of the developmental costs. Of course, they don't have total developmental control but they do get a seat at the table. -Any gaps between the open source {admiral} package and the proprietary Roche workflow were bridged by the internal {admiralRoche} package. +Any gaps between the open source [{admiral}](https://github.com/pharmaverse/admiral) package and the proprietary Roche workflow were bridged by the internal {admiralRoche} package. The switch towards a more language agnostic platform, and open source languages specifically, opens the door to a broad population of university graduates with diverse backgrounds. I personally would not have considered this position five years ago due to a misalignment of skills and job requirements. @@ -125,7 +126,7 @@ The possibility for statistical programmers to pivot towards developing software It is this transformation that is reflected by the choice of Roche to re-brand statistical programmers as analytical data scientists. The fact that cross-industry development is being advocated for really lets programmers expand their network outside of their company. -The {admiral} project serves as a testament to the power of collaborative open-source development and the potential it holds for the future of work in this industry. +The [{admiral}](https://github.com/pharmaverse/admiral) project serves as a testament to the power of collaborative open-source development and the potential it holds for the future of work in this industry. diff --git a/posts/2023-07-20_cross_company_dev/project_board.png b/posts/2023-07-20_cross_company_dev/project_board.png new file mode 100644 index 00000000..1eae6405 Binary files /dev/null and b/posts/2023-07-20_cross_company_dev/project_board.png differ