Sean Davis @ NCI

November Bioinformatics and Data Science Papers

I am starting to make a short list of papers that interested me for the month. In creating this list, I make no claims about these being the “best” papers, the most interesting, or even that they are “good” papers. The list simply serves as an external brain for me and may include some papers that are of interest to others. Besides the usual single manuscripts, November publications included a complete issue of Cancer Research focused on computational resources.

A computable Bioconductor build report

Bioconductor spends a substantial amount of effort to build its catalog of software each day. Reporting of these results is critical for developers, users, and project leaders to understand the software “health” of the project. The Bioconductor build reports are generally available as html pages that are navigable with bookmarks and link out to detailed reports of errors, etc. However, the build reports are not readily computable, so mining the reports, automated processing by developers, and learning about failure modes automatically is challenging.

Agricultural genomics may benefit from human genomic data and software engineering

As a government employee, I have been given some fantastic opportunities to interact with other government employees and agencies doing really important research in service to the country. Over the past couple of days, I have been attending a great symposium to provide an updated Blueprint for animal genetics and genomics. Discussion was wide-ranging, but largely focused on genomics, informatics, and translation to and from phenotypes. High-throughput phenotyping (think wearables for plants and cows and drone videos of cattle herds) seems like a growth area.

Approaches to accessing data

I have been attending the biannual Clinical Informatics for Cancer Centers (CI4CC) conference and there has been a fair amount of dicussion of as a resource for enhancing patient engagement, trial recruitment, and results reporting. There are a number of approaches to search and access in bulk data. The ones that I address here are: The CTRP RESTful API. The API. The Access to Aggregate Content of ClinicalTrials.

Hello R Markdown

R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see You can embed an R code chunk like this: summary(cars) ## speed dist ## Min. : 4.0 Min. : 2.00 ## 1st Qu.:12.0 1st Qu.: 26.00 ## Median :15.0 Median : 36.00 ## Mean :15.4 Mean : 42.98 ## 3rd Qu.