Research Tools

How to get started with Git for biomedical researchers

/ Anirvan Chatterjee

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

/ melissatelli / 1 Comment

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

/ leslieyuan / 1 Comment

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 →

Social Networks for Academics Proliferate, Despite Some Scholars Doubts

/ leslieyuan

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

/ Anirvan Chatterjee / 3 Comments

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?

/ leslieyuan / 1 Comment

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.

Take Advantage of Web-Based Tools to Present Complex Data

/ Katja Reuter

Research to Action published a great overview article that highlights an “ever-growing open-data source for development statistics in the fields of economics, healthcare, education, social science, technology,” and more.

Including data and statistics within research findings can enhance their impact, however, large tables or spreadsheets of numbers take time to decipher and sometimes the true meaning behind the data itself can be misinterpreted.

Here are some of the tools that the article points out:

  • StatPlanet: browser-based interactive data visualization and mapping application to create a wide range of visualizations, from simple Flash maps to more advanced infogrpahics.
  • Xtimeline:  to create your own timelines of data.
  • Gap Minder: to upload data and create an interactive motion charts and graphs.
  • Creately:  to use Online Diagramming software – purpose built for team collaboration.
  • Google Chart Tools: lets you include constantly changing research data sourced online. Google has also released Fusion Tables where you can share, discuss and track your charts and graphs with specific people online.
  • Tagcrowd: to upload texts and highlight the most common concepts. The clouds can be exported as images and inserted in a website or power point presentation.
  • Wordle: similar to tagcloud; lets you create images out of key phrases and words relevant to your research, great for using in PowerPoint presentations.
  • Tableau: a free Windows-only software for creating colourful data visualisations.

View all and read the original article