Adding sections

inst/WORDLIST.txt

@@ -323,3 +323,5 @@ Knoph
 Nordisk
 Novo
 Siggaard
+pharma
+reproducibility

posts/2023-08-30_pharmaverse_story/pharmaverse_story.qmd

@@ -22,6 +22,8 @@ long_slug <- "2023-08-30_pharmaverse_story"
 
 Pharmaverse: from motivation to present
 
+**Human history and pharmaverse context**
+
 Since the Australian Aboriginal, the earliest peoples recorded to have inhabited the Earth and who have been in Australia for at least 65,000 to 80,000 years ([Encyclopædia Britannica](https://www.britannica.com/topic/Australian-Aboriginal)), human beings live in group.
 Whether to protect yourself, increase your life expectancy or simply share tasks.
 
@@ -39,13 +41,15 @@ They are the founders of [pharmaverse](https://pharmaverse.org/), members of its
 If you are not familiar with this pipeline, the important thing to know is that, in a nutshell, pharmaceutical companies must follow a bunch of standardized procedures and formats (from Clinical Data Interchange Standards Consortium, [CDISC](https://www.cdisc.org/)) when submitting clinical results to Health Authorities.
 Focus on this: **different** companies seeking the **same** standards for outputs.
 
-Paraphrasing Ross presentation in [R/Pharma 2022](https://www.youtube.com/watch?v=APMDOS4v9Hk) and thinking of the development of a new drug, we are talking about a "post-competitive" scenario: the drug has already been discovered and the companies should "just" produce and deliver standardized results.
+Paraphrasing Ross *Breaking boundaries through open-source collaboration* presentation in [R/Pharma 2022](https://www.youtube.com/watch?v=APMDOS4v9Hk) and thinking of the development of a new drug, we are talking about a "post-competitive" scenario: the drug has already been discovered and the companies should "just" produce and deliver standardized results.
+
+**Clinical reporting outputs**
 
 Rationally, we can say that companies face the same challenges in these steps of the process.
-Irrationally, we can also say they were working in silos on that.
+Irrationally, we can also say they were working in silos on that before 2018.
 Just as Isaac Newton and Gottfried W. Leibniz [independently developed the theory of infinitesimal calculus](https://en.wikipedia.org/wiki/History_of_calculus), pharmaceutical companies were independently working on R solutions for this pipeline.
 
-But in 2018, on August 16 and 17, they gathered at the first edition of [R/Pharma conference](https://rinpharma.com/) to discuss R and open-source tooling for drug development (the reasons why open-source is an advantageous approach can be found in this [post](https://pharmaverse.github.io/blog/posts/2023-07-20_cross_company_dev/cross_industry_dev.html) written by Stefan Thoma).
+But on August 16 and 17 of the mentioned year above, they gathered at the first edition of [R/Pharma conference](https://rinpharma.com/) to discuss R and open-source tooling for drug development (the reasons why open-source is an advantageous approach can be found in this [post](https://pharmaverse.github.io/blog/posts/2023-07-20_cross_company_dev/cross_industry_dev.html) written by Stefan Thoma).
 And according to Isabela Velásquez's article, [Pharmaverse: Packages for clinical reporting workflows](https://posit.co/blog/pharmaverse-packages-for-clinical-reporting-workflows/), one of the most popular questions in this conference was "Is the package code available or on [CRAN](https://cran.r-project.org/)?".
 
 Well, many of them were.
@@ -60,6 +64,8 @@ And that took to another two questions:
 So, again, companies re-started to working in silos to find those answers.
 But now, in collaborative silos and with common goals: create extremely useful packages to solve pharmaceutical-specific gaps once and solve them well!
 
+**First partnerships**
+
 In 2020, Michael Stackhouse and Michael Rimler talked and formed a partnership between Atorus and GSK to develop a few more packages, including [*metacore*](https://github.com/atorus-research/metacore), to read, store and manipulate metadata for ADaMs/SDTMs in a standardized object; [*xportr*](https://github.com/atorus-research/xportr), to create submission compliant SAS transport files and perform pharma specific dataset level validation checks; and [*logrx*](https://github.com/pharmaverse/logrx) (ex-*timber*), to build log to support reproducibility and traceability of an R script.
 
 Around the same time, Thomas Neitmann (actual Denali Therapeutics, ex-Roche) and Rimler discovered that both were working with ADaM in R, so Ross and Rimler saw an opportunity there and GSK started their partnership with Roche to build and release [*admiral*](https://github.com/pharmaverse/admiral) package.
@@ -68,6 +74,8 @@ The idea of working together, the sense of community, and the appetite from orga
 
 Janssen had a huge effort in building R capabilities going on as well, by releasing [*tidytlg*](https://github.com/pharmaverse/tidytlg) and [*envsetup*](https://github.com/pharmaverse/envsetup)), so eventually Rimler, Stackhouse and Ross formalized [pharmaverse](https://pharmaverse.org/) and formed the council, adding in Sumesh (Janssen) and Ari Siggaard Knoph (Novo Nordisk) later joined as the fifth council member.
 
+**Release, growth and developments**  
+
 At the end of their presentation ["Closing the Gap: Creating an End to End R Package Toolkit for the Clinical Reporting Pipeline."](https://www.youtube.com/watch?v=NW9qp5QOlIU), in [R/Pharma 2021](https://rinpharma.com/event/rinpharma2021/), Ben Straub's (GSK) and Eli Miller's (Atorus) welcomed the community to the [pharmaverse](https://pharmaverse.org/), a new group of packages developed by various pharmaceutical companies to support open-source clinical workflows.
 
 From the outset, the name [pharmaverse](https://pharmaverse.org/) was chosen so that it could be a neutral home, unrelated to any company.
@@ -81,6 +89,7 @@ Despite all its structure, it is impossible to say that we have a single solutio
 Instead, it is necessary to accept viable tools fitting different pathways into [pharmaverse](https://pharmaverse.org/) to direct and give people options as to what might work for them.
 After all, even though we live together as a community, we still have our own unique internal problems.
 
+
 ![Sample of pharmaverse packages](logos.png)
 
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