From d4ad089ef02fef43b344da75766d5b67f46668cb Mon Sep 17 00:00:00 2001 From: Rita Pecuch Date: Mon, 29 Sep 2025 17:00:51 -0400 Subject: [PATCH 1/6] add skeleton for industry talk review blog post --- site/posts/industry-talk-review/index.ipynb | 64 +++++++++++++++++++ site/posts/industry-talk-review/index.qmd | 37 +++++++++++ .../posts/industry-talk-review/references.bib | 28 ++++++++ 3 files changed, 129 insertions(+) create mode 100644 site/posts/industry-talk-review/index.ipynb create mode 100644 site/posts/industry-talk-review/index.qmd create mode 100644 site/posts/industry-talk-review/references.bib diff --git a/site/posts/industry-talk-review/index.ipynb b/site/posts/industry-talk-review/index.ipynb new file mode 100644 index 0000000..eb80204 --- /dev/null +++ b/site/posts/industry-talk-review/index.ipynb @@ -0,0 +1,64 @@ +{ + "cells": [ + { + "cell_type": "raw", + "metadata": {}, + "source": [ + "---\n", + "title: \"Industry Talk Review\"\n", + "author: \"Rita Pecuch\"\n", + "date: \"2025-03-29\"\n", + "categories: [review, git, pharmaceuticals]\n", + "# format:\n", + "# html:\n", + "# toc: true\n", + "# code-fold: true\n", + "bibliography: references.bib\n", + "# TODO: add the csl file and uncomment\n", + "# csl: apa.csl # for APA style citation\n", + "toc: TRUE\n", + "toc-title: \"Table of Contents\"\n", + "toc-depth: 5\n", + "---" + ], + "id": "a8052c25" + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Introduction\n", + "\n", + "Test reference @esteva2019guide\n", + "\n", + "# Search Strategy\n", + "\n", + "# Major Themes\n", + "\n", + "## Theme 1\n", + "\n", + "## Theme 2\n", + "\n", + "# Key Findings\n", + "\n", + "# Conclusion\n", + "\n", + "# References\n", + "\n", + "\n", + "```{bibliography}\n", + "```" + ], + "id": "f904cdc1" + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} \ No newline at end of file diff --git a/site/posts/industry-talk-review/index.qmd b/site/posts/industry-talk-review/index.qmd new file mode 100644 index 0000000..c0761d8 --- /dev/null +++ b/site/posts/industry-talk-review/index.qmd @@ -0,0 +1,37 @@ +--- +title: "Industry Talk Review" +author: "Rita Pecuch" +date: "2025-03-29" +categories: [review, git, pharmaceuticals] +# format: +# html: +# toc: true +# code-fold: true +bibliography: references.bib +# TODO: add the csl file and uncomment +# csl: apa.csl # for APA style citation +toc: TRUE +toc-title: "Table of Contents" +toc-depth: 5 +--- + +# Introduction + +Test reference @esteva2019guide + +# Search Strategy + +# Major Themes + +## Theme 1 + +## Theme 2 + +# Key Findings + +# Conclusion + +# References + +```{bibliography} +``` diff --git a/site/posts/industry-talk-review/references.bib b/site/posts/industry-talk-review/references.bib new file mode 100644 index 0000000..d426cf7 --- /dev/null +++ b/site/posts/industry-talk-review/references.bib @@ -0,0 +1,28 @@ +@article{esteva2019guide, + title={A guide to deep learning in healthcare}, + author={Esteva, Andre and Chou, Kangchen and Yeung, Serena and Naik, Nikhil and Madani, Ali and Mottaghi, Ali and Liu, Yun and Topol, Eric}, + journal={Nature medicine}, + volume={25}, + number={1}, + pages={24--29}, + year={2019}, + publisher={Nature Publishing Group} +} + +@article{rajkomar2018scalable, + title={Scalable and accurate deep learning with electronic health records}, + author={Rajkomar, Alvin and et al.}, + journal={NPJ Digital Medicine}, + volume={1}, + number={1}, + pages={18}, + year={2018}, + publisher={Nature Publishing Group} +} + +@article{holzinger2017we, + title={What do we need to build explainable AI systems for the medical domain?}, + author={Holzinger, Andreas and et al.}, + journal={arXiv preprint arXiv:1712.09923}, + year={2017} +} From 70d8259e10a9355363387487fbc8c58eaeda3aea Mon Sep 17 00:00:00 2001 From: Rita Pecuch Date: Tue, 30 Sep 2025 08:39:08 -0400 Subject: [PATCH 2/6] added introduction draft and start of search strategy --- site/posts/industry-talk-review/index.ipynb | 8 ++++---- site/posts/industry-talk-review/index.qmd | 12 ++++++------ 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/site/posts/industry-talk-review/index.ipynb b/site/posts/industry-talk-review/index.ipynb index eb80204..acf1126 100644 --- a/site/posts/industry-talk-review/index.ipynb +++ b/site/posts/industry-talk-review/index.ipynb @@ -13,7 +13,7 @@ "# html:\n", "# toc: true\n", "# code-fold: true\n", - "bibliography: references.bib\n", + "# bibliography: references.bib\n", "# TODO: add the csl file and uncomment\n", "# csl: apa.csl # for APA style citation\n", "toc: TRUE\n", @@ -21,7 +21,7 @@ "toc-depth: 5\n", "---" ], - "id": "a8052c25" + "id": "18a4a0be" }, { "cell_type": "markdown", @@ -29,7 +29,7 @@ "source": [ "# Introduction\n", "\n", - "Test reference @esteva2019guide\n", + "Test reference \n", "\n", "# Search Strategy\n", "\n", @@ -49,7 +49,7 @@ "```{bibliography}\n", "```" ], - "id": "f904cdc1" + "id": "858e852d" } ], "metadata": { diff --git a/site/posts/industry-talk-review/index.qmd b/site/posts/industry-talk-review/index.qmd index c0761d8..5aaf504 100644 --- a/site/posts/industry-talk-review/index.qmd +++ b/site/posts/industry-talk-review/index.qmd @@ -7,9 +7,6 @@ categories: [review, git, pharmaceuticals] # html: # toc: true # code-fold: true -bibliography: references.bib -# TODO: add the csl file and uncomment -# csl: apa.csl # for APA style citation toc: TRUE toc-title: "Table of Contents" toc-depth: 5 @@ -17,10 +14,14 @@ toc-depth: 5 # Introduction -Test reference @esteva2019guide +The usage of Git in clinical programming within the pharmaceutical industry has been steadily increasing over the last several years. Beyond the discussions of our PHUSE working group, several talks at recent industry events have showcased how various companies are leveraging this technology. # Search Strategy +The search for materials spanned a few major conferences over the past few years. The PHUSE archive was the primary resource utilized, as heavy representation from pharmaceutical companies is customary for PHUSE events. In addition, talks from the Posit Conference were evaluated, as this is a major open-source technology event which typically includes at least a small degree of representation from the pharmaceutical industry. + +R/Pharma + # Major Themes ## Theme 1 @@ -33,5 +34,4 @@ Test reference @esteva2019guide # References -```{bibliography} -``` + From 443a82b63bb1c3e9df7be614bd2989e69ad9777c Mon Sep 17 00:00:00 2001 From: Rita Pecuch Date: Tue, 30 Sep 2025 14:44:17 -0400 Subject: [PATCH 3/6] added citations for papers that will be reviewed --- site/posts/industry-talk-review/index.qmd | 34 +++++++++++++++++++---- 1 file changed, 28 insertions(+), 6 deletions(-) diff --git a/site/posts/industry-talk-review/index.qmd b/site/posts/industry-talk-review/index.qmd index 5aaf504..62dac71 100644 --- a/site/posts/industry-talk-review/index.qmd +++ b/site/posts/industry-talk-review/index.qmd @@ -3,10 +3,6 @@ title: "Industry Talk Review" author: "Rita Pecuch" date: "2025-03-29" categories: [review, git, pharmaceuticals] -# format: -# html: -# toc: true -# code-fold: true toc: TRUE toc-title: "Table of Contents" toc-depth: 5 @@ -18,9 +14,9 @@ The usage of Git in clinical programming within the pharmaceutical industry has # Search Strategy -The search for materials spanned a few major conferences over the past few years. The PHUSE archive was the primary resource utilized, as heavy representation from pharmaceutical companies is customary for PHUSE events. In addition, talks from the Posit Conference were evaluated, as this is a major open-source technology event which typically includes at least a small degree of representation from the pharmaceutical industry. +The search for materials spanned the 2025 PHUSE archive, as heavy representation from pharmaceutical companies is customary for PHUSE events. -R/Pharma +The aim is not only to summarize how companies are leveraging Git, but to evaluate applications of open-source technology and propose how Git can be useful. # Major Themes @@ -34,4 +30,30 @@ R/Pharma # References +In paper reference template - white papers: +(Furst & DeMillo, 2006) +Andhale, S.H., Sood, S. (2025). Harnessing the Power of R Shiny in a GxP compliant and validated manner for clinical trials use [White paper OS3464]. Sycamore Informatics India Private Limited. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_OS10.pdf + +Arancibia, B. (2025). What R We Counting? The Quest to Quantify R Usage in Biostatistics Organizations [White paper OS02]. GSK. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_OS02.pdf + +Ching, E. (2025). Learning to skate, pedal, and drive – Change leadership in the world of Agile delivery [White paper PD02]. GSK. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_PD02.pdf + +Hume, S. (2025). A Technical Roadmap Defining CDISC's Path to End-to-End Automation [White paper DS05]. CDISC. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_DS05.pdf + +Kim, J. (2025). The changes in the job of statistical programmer in the +pharmaceutical industry [White paper ET07]. Pfizer Inc. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_ET07.pdf + +Liao, C. (2025). Building Rome in a Few Months: How Open Source Technologies Empower Small Pharma [White paper OS07]. Recursion. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_OS07.pdf + +Opalka, A. (2025). GitLab vs GitHub: The Battle of the Repositories [Poster PP05]. Roche. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/CSS/EU/Utrecht/POS_PP05.pdf + +Patel, J. (2025). Evaluation of Open-Source Technologies in Clinical Trial Reporting [White paper PP15]. AstraZeneca US Biometric. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_PP15.pdf + +Shi, T., Song, L., Nomula, V.K. (2025). Implementation of a risk-governed, reproducible, and collaborative R workflow for Real World Evidence Projects [White paper PP27]. Merck & Co., Inc. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_PP27.pdf + +Tahiliani, K., Jain, A. (2025). A Journey Through an Innovative Approach to Migration of Legacy System to New Multilingual Statistical Computing Environment (SCE). GSK. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_ET21.pdf + +Veríssimo, A., Viyash, V. (2025). Accelerating Shiny Application Development and Validation with Rhino [White paper OS15]. Appsilon. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_OS15.pdf + +Zhang, P., Chen, J., Yang, F., Chang, V., Lee, J. (2025). Generate Clinical Study Report (CSR) document using {quarto} and {shiny} [White paper OS06]. CIMS Global. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_OS06.pdf From 414c384a4e4e342616be744a497166a726f734ed Mon Sep 17 00:00:00 2001 From: Rita Pecuch Date: Wed, 1 Oct 2025 10:55:33 -0400 Subject: [PATCH 4/6] added notes from first paper review --- site/posts/industry-talk-review/index.qmd | 40 ++++++++++++++++++++--- 1 file changed, 35 insertions(+), 5 deletions(-) diff --git a/site/posts/industry-talk-review/index.qmd b/site/posts/industry-talk-review/index.qmd index 62dac71..d736821 100644 --- a/site/posts/industry-talk-review/index.qmd +++ b/site/posts/industry-talk-review/index.qmd @@ -20,9 +20,42 @@ The aim is not only to summarize how companies are leveraging Git, but to evalua # Major Themes -## Theme 1 +## Increasing Usage of Open-Source Programming -## Theme 2 +(Andhale & Sood, 2025) +- R is powerful language for statistical modeling and hypothesis testing within the industry +- Clean data, apply stats models, and implement ML algorithms all within single platform +- Shiny allows visualizing large datasets that are common in this industry, and get actionable insights +- HTML, CSS, and JS knowledge not required --> so lowered barrier for getting more people into open-source programming +- Interactive elements for deeper data exploration +- Integrate data from several sources, across studies, leverage historical data +- More flexibility to meet diverse needs of stakeholders +- Scalability important for exponentially increasing amounts of data due to multicenter international trials + +## Rise of Agile Methologies + +(Andhale & Sood, 2025) +- becoming more common +- Real-time communication and iterative progress in workflows + +## Need for Version Control + +(Andhale & Sood, 2025) +- Important to support agile and collaborative development +- Particulary useful for complex projects + + +## GxP Compliance + +(Andhale & Sood, 2025): +- All open source packages used for regulatory submissions must be validated (proven to meet regulatory standards), documented, and controlled in SCE +- Must be traceability of all code changes +- Allows reproducibility of all versions of code + +## Collaborative Learning Communities + +(Andhale & Sood, 2025) +- For R programming # Key Findings @@ -30,9 +63,6 @@ The aim is not only to summarize how companies are leveraging Git, but to evalua # References -In paper reference template - white papers: -(Furst & DeMillo, 2006) - Andhale, S.H., Sood, S. (2025). Harnessing the Power of R Shiny in a GxP compliant and validated manner for clinical trials use [White paper OS3464]. Sycamore Informatics India Private Limited. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_OS10.pdf Arancibia, B. (2025). What R We Counting? The Quest to Quantify R Usage in Biostatistics Organizations [White paper OS02]. GSK. https://phuse.s3.eu-central-1.amazonaws.com/Archive/2025/Connect/US/Orlando/PAP_OS02.pdf From 16256f1c839ba38865d533d7660dacea0d3f0751 Mon Sep 17 00:00:00 2001 From: Rita Pecuch Date: Wed, 1 Oct 2025 10:57:03 -0400 Subject: [PATCH 5/6] removed .pynb file --- site/posts/industry-talk-review/index.ipynb | 64 --------------------- 1 file changed, 64 deletions(-) delete mode 100644 site/posts/industry-talk-review/index.ipynb diff --git a/site/posts/industry-talk-review/index.ipynb b/site/posts/industry-talk-review/index.ipynb deleted file mode 100644 index acf1126..0000000 --- a/site/posts/industry-talk-review/index.ipynb +++ /dev/null @@ -1,64 +0,0 @@ -{ - "cells": [ - { - "cell_type": "raw", - "metadata": {}, - "source": [ - "---\n", - "title: \"Industry Talk Review\"\n", - "author: \"Rita Pecuch\"\n", - "date: \"2025-03-29\"\n", - "categories: [review, git, pharmaceuticals]\n", - "# format:\n", - "# html:\n", - "# toc: true\n", - "# code-fold: true\n", - "# bibliography: references.bib\n", - "# TODO: add the csl file and uncomment\n", - "# csl: apa.csl # for APA style citation\n", - "toc: TRUE\n", - "toc-title: \"Table of Contents\"\n", - "toc-depth: 5\n", - "---" - ], - "id": "18a4a0be" - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Introduction\n", - "\n", - "Test reference \n", - "\n", - "# Search Strategy\n", - "\n", - "# Major Themes\n", - "\n", - "## Theme 1\n", - "\n", - "## Theme 2\n", - "\n", - "# Key Findings\n", - "\n", - "# Conclusion\n", - "\n", - "# References\n", - "\n", - "\n", - "```{bibliography}\n", - "```" - ], - "id": "858e852d" - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} \ No newline at end of file From dde4ab5c4f8f94fef64786bda2e550114ea24a7f Mon Sep 17 00:00:00 2001 From: Rita Pecuch Date: Wed, 1 Oct 2025 10:57:52 -0400 Subject: [PATCH 6/6] removed old external references file --- .../posts/industry-talk-review/references.bib | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 site/posts/industry-talk-review/references.bib diff --git a/site/posts/industry-talk-review/references.bib b/site/posts/industry-talk-review/references.bib deleted file mode 100644 index d426cf7..0000000 --- a/site/posts/industry-talk-review/references.bib +++ /dev/null @@ -1,28 +0,0 @@ -@article{esteva2019guide, - title={A guide to deep learning in healthcare}, - author={Esteva, Andre and Chou, Kangchen and Yeung, Serena and Naik, Nikhil and Madani, Ali and Mottaghi, Ali and Liu, Yun and Topol, Eric}, - journal={Nature medicine}, - volume={25}, - number={1}, - pages={24--29}, - year={2019}, - publisher={Nature Publishing Group} -} - -@article{rajkomar2018scalable, - title={Scalable and accurate deep learning with electronic health records}, - author={Rajkomar, Alvin and et al.}, - journal={NPJ Digital Medicine}, - volume={1}, - number={1}, - pages={18}, - year={2018}, - publisher={Nature Publishing Group} -} - -@article{holzinger2017we, - title={What do we need to build explainable AI systems for the medical domain?}, - author={Holzinger, Andreas and et al.}, - journal={arXiv preprint arXiv:1712.09923}, - year={2017} -}