- WebGraph — a framework for graph compression aimed at studying web graphs. It provides simple ways to manage very large graphs, exploiting modern compression techniques. (via Ben Lorica)
- Learn to Program with Minecraft Plugins — You’ll need to add features to the game itself: learn how to build plugins for your own Minecraft server using the Java programming language. You don’t need to know anything about programming to get started—-this book will teach you everything you need to know! Shameless Christmas stocking bait! (via Greg Borenstein)
- In Search of Perfection, Young Adults Turn to Adderall at Work (Al Jazeera) — “Adderall is just the tip of the iceberg,” Essig said. “There are lots more drugs coming down the pike. The way we set up our cultural model for dealing with psychologically performance-enhancing drugs is a real serious question.”
- Explain Shell — uses parsed manpages to explain a shell commandline. (via Tracy K Teal)
Zombie Drones, Algebra Through Code, Data Toolkit, and Crowdsourcing Antibiotic Discovery
- Skyjack — drone that takes over other drones. Welcome to the Malware of Things.
- Bootstrap World — a curricular module for students ages 12-16, which teaches algebraic and geometric concepts through computer programming. (via Esther Wojicki)
- Harvest — open source BSD-licensed toolkit for building web applications for integrating, discovering, and reporting data. Designed for biomedical data first. (via Mozilla Science Lab)
- Project ILIAD — crowdsourced antibiotic discovery.
Open source communities to help find the next blockbuster drug
Big drug companies are not what they used to be. It is harder to find new drug candidates, to test them, and to get them approved than ever before. Drugs that are “mere chemicals” are becoming more and more complex. Frequently, new drugs require DNA interaction, which requires them to be manufactured through a mostly automated cellular process rather than just mixing the right components in the right order. Just the changes to the refrigeration requirements for these new drugs represents a challenge to drug manufacturers, pharmacies and hospitals.
Combined, these difficulties create a combustible business environment that can ignited by the pressure of expiring patents. Experts estimate that the approval process ensures that a drug company actually gets only about 12 years of exclusivity before a 20-year patent wears off. So in pharma-land, the march of popular medications to generic status forces the original developers into the famous Innovators Dilemma. Most companies face competition from the generic versions of their own previous work.
Can open data dominate biological science as open source has in software?
To move from a hothouse environment of experimentation to the mainstream of one of the world's most lucrative and tradition-bound industries, Sage Bionetworks must aim for its nucleus: rewards and incentives. Comparisons to open source software and a summary of tasks for Sage Congress.
The Vioxx problem is just one instance of the wider malaise afflicting the drug industry. Managers from major pharma companies expressed confidence that they could expand public or "pre-competitive" research in the direction Sage Congress proposed. The sector left to engage is the one that's central to all this work–the public.
Report from a movement that believes in open source and open data in science
Through two days of demos, keynotes, panels, and breakout sessions, Sage Congress brought its vision to a high-level cohort of 230 attendees from universities, pharmaceutical companies, government health agencies, and others who can make change in the field.