Open Source Software for Scientific Applications

The ​BioUno​ open­ source project seeks to improve scientific application automation, performance, reproducibility, usability, and management by applying and extending software engineering (SE) best practices in the field of scientific research applications. Deliverables from the project have found a variety of applications in life­science research (bioinformatics, genetics, drug discovery).

  • We ​explore​ and apply​ best practices in software engineering to support the project mission
  • We ​develop extensions​ to established SE tools, frameworks and technologies that directly ​ support​ or indirectly ​enhance​ scientific applications.
  • We ​develop APIs​ and ​integration​ points that empower scientific applications through the use
  • We promote ​collaboration and reuse​ through contributing to existing open source projects
  • We ​educate users​ through blog, wiki, and presentations on the application of SE best practices in scientific applications
  • We ​advocate​ with software engineers for enabling SE tools and frameworks for use by scientists

Read more about the project, its mission, objectives, motivations and strategy.

Recent Posts

BioUno meeting 2016-11-18

less than 1 minute read

Participants: Bruno P. Kinoshita and Ioannis K. Moutsatsos. 2016-11-18 08:00 PM UTC using Google Hangouts.

Jenkins: Documenting Data with Metadata

5 minute read

Data without associated annotation and metadata (documentation describing the data) is of little lasting value 1. It is imperative that each dataset used for...

BioUno meeting 2016-07-27

2 minute read

Participants: Bruno P. Kinoshita and Ioannis K. Moutsatsos. 2016-07-27 08:00 PM UTC using Google Hangouts.

Is it Wow or Just about Time?

6 minute read

We all know and love Jenkins despite some of its historical quirks. The community is now on a march to introduce some new concepts and a more modern UI that ...

Creating a Jenkins Data Science Platform

6 minute read

Having worked with Jenkins-CI in the life sciences context for the last few years, I am finding that Jenkins satisfies key requirements of a robust framework...

From Uno-Choice to Active Choices

4 minute read

More than a year ago I approached Bruno via a series of posts on the BioUno developer’s forum and discussed my frustration with the available Jenkins user in...

Java DRMAA API — part 2

1 minute read

This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec.

Consistent Reports for Data Analysis

8 minute read

When you use Jenkins for analytics it is important to deliver consistent analysis reports from each build. There are a few different ways that you can create...

Java DRMAA API — part 1

4 minute read

This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec. PBS is a type of batch server, or distributed r...

Playing with BioJS

1 minute read

In the post entitled The Secret of Building a scientific community, Manuel Corpas describe his experiences coordinating the BiosJS project. It is a great w...

rOpenSci in Jenkins

2 minute read

rOpenSci is an Open Data project. It has many R packages that access several data repositories. In this post we will demonstrate how to use rOpenSci taxize p...

DNADigest Hackday and Metadata

1 minute read

DNADigest held a free Hackday this past Saturday, April 5th, in London. Luckily they also live transmitted the event via Internet, and it was definitely wor...

More plug-ins released

less than 1 minute read

In the past days two more plug-ins were released to our update center. The plug-ins are CLUMPP plug-in and Structure Harvester plug-in. Before that the fir...

The BioUno blog is live

less than 1 minute read

We are migrating our old web site to GitHub pages. We expect that it will make typos, new docs and suggestions easier to get fixed, merged and released. Fee...