How to get started with Git for biomedical researchers

Learning basic Git is a pretty essential skill for biomedical researchers sharing code—and increasingly, data—with others.

Thankfully, there’s a wealth of helpful guides out there on how to get started. Here are 4 resources we recommend:

  1. Why use Git? Skim “Git can facilitate greater reproducibility and increased transparency in science” by Karthik Ram
  2. Are you a visual learner? Watch Data School’s Git and GitHub videos for beginners
  3. Want to learn by doing, and already have Git on your command line? Begin with Software Carpentry’s self-guided lesson on how to get started with Git
  4. Want to work with others? You’ll probably want to set up a free account on Github (the most commonly used Git hosting/collaboration site) — and if you want to upgrade, you can take advantage of their education discounts

 

Teenage Migraine Researcher Uses Mobile Technology to Enhance Study

A new clinical trial for adolescent migraine is underway, and it’s harnessing the power of consumer technology to collect better data and make study participation easier. The BRAiN-M Study, which is examining whether melatonin (a natural supplement) is effective in preventing teenage migraine, uses Fitbit devices and an online “headache diary” to collect data from study participants remotely.

Besides trying to figure out how to prevent teenage migraine, the study’s lead investigator, Dr. Amy Gelfand of UCSF, is looking to make pediatric migraine clinical trials more inclusive and accessible. Continue reading

We’ve completed our NSF Grant! UCSF Profiles and its use by external partners

UCSF Profiles is an example of a Research networking system (RNS). These systems provide automated aggregation and mining of information to create profiles and networks of the people that make up an academic institution. RNS’s have in effect, become a new kind of ‘front door’ for the university, providing access to the university’s intellectual capital in a manner previously unattainable — i.e. one focused on expertise rather than schools or departments, thus intermingling experts regardless of where they’re officially housed. Against this backdrop, we wanted to understand how such a tool might enhance access to academic expertise by external partners, specifically industry, and improve UCSF’s response to industry interest. Continue reading

Wanna Play? Computer Gamers Help Push Frontier Of Brain Research

berger-cube_dendrites-1Here is a fascinating NPR news story about using people’s addiction to computer games to advance science.

People can get pretty addicted to computer games. By some estimates, residents of planet Earth spend 3 billion hours per week playing them. Now some scientists are hoping to make use of all that human capital and harness it for a good cause. Read more…

Social Networks for Academics Proliferate, Despite Some Scholars Doubts

Here’s an article with an overview of online products out there for research social networking;  the big gap in the article is that no institutional products are included such as Profiles, VIVO, etc. This is noted in one of the comments at the end, by Titus Schleyer.

That aside, there are interesting opinions in this piece, a few clipped below, and perhaps pointing to the current status of the space,  where the sweet spot has not yet been found.  

“After six years of running Zotero, it’s not clear that there is a whole lot of social value to academic social networks,” says Sean Takats, the site’s director, who is an assistant professor of history at George Mason University. “Everyone uses Twitter, which is an easy way to pop up on other people’s radar screens without having to formally join a network.” 

Scholars aren’t interested in sharing original ideas on such sites, [Christopher Blanchard, an adjunct professor of community and regional planning at Boise State University] now believes, “because they’re afraid they’ll be ripped off” and because they simply don’t have the time.

“We have thousands of new discussions taking place every day—scientists helping scientists without getting anything for it,” [Dr. Madisch, of ResearchGate] says. “Three years ago, people were smiling at me and saying that scientists aren’t social. They won’t share information. They were wrong.”

Social Networks for Academics Proliferate, Despite Some Scholars Doubts – Technology – The Chronicle of Higher Education.

AMIA 2012 Joint Summit: a report back in tweets

Eric, Leslie, and I from CTSI at UCSF’s Virtual Home team spent the past three days at the AMIA 2012 Joint Summit in San Francisco.

Here’s some of what was happening on the researcher networking, social networking, knowledge representation fronts, and public search front, via Twitter:

Other tweets that caught my eye from the rest of the conference:

Collaboration Success Wizard — want to test to see if your geographically distributed team is poised for success?

Collaboration Success Wizard.

Check this out … looks really interesting!

Here’s the description from the site:

Once a project is approved to participate [to use the Wizard], we send invitation e-mails to all the project members. The Wizard is an online survey that takes about 30 minutes. Each individual involved in the project should take the survey independently. The more project members who take the survey, the better the data!

And yes – it’s free!

At the end of the survey each participant can see a personalized individual report that contains feedback based on their answers and our research. This report is available immediately, and summarizes both the strong points and the issues at risk for the target collaboration.