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


Balancing the benefits and risks in using Cloud Technology for Research

Contributed by Jamie Lam, Data Security Compliance Manager, UCSF School of Medicine

Cloud technology offers many benefits to researchers, such as:

  • ease of use,
  • rapid deployment, and
  • reduced costs.

At the same time, there are also some hidden implications to using a cloud service provider, including security obligations that may not be well understood.

While a well-designed cloud computing system can be safer than traditional client-server systems, when you are considering a cloud service, you must understand the benefits and risks, as well as your responsibilities in keeping sensitive data secure.

A couple of important points:

1) UC has standard contracts used with providers that protect our institutions’ security and assets. You should always work with procurement so they can ensure that the appropriate agreement is in place.

2) If disruption to services will negatively impact your research or operations, you should negotiate a Service Level Agreement (SLA) based on your needs.

However, don’t just rely on the signed contracts – you should always vet the vendors to confirm that they really are protecting our patients and our reputation.

UCSF has many resources to help you select the right vendor and ensure that your application and sensitive data are secure:

Interested in understanding more about Cloud Services and their benefits and risks? Take a look at this presentation by the School of Medicine Data Security Compliance Program: Securing Data in the Cloud

RNS SEO 2016: How 90 research networking sites perform on Google — and what that tells us

RNS SEO 2015 header

Research networking systems (RNS) like Vivo, Profiles, and Pure are often sometimes undiscoverable by real users because of poor search engine optimization (SEO).

Last year, we released RNS SEO 2015, the first-ever report describing how RNS performs in terms of real-world discoverability on Google.

We re-ran our analysis for 2016, to see which of 90 different research networking sites has the highest proportion of their people pages among the top 3 search results on Google.

1. Methodology

  • Pick 90 different VIVO, Profiles, Pure, and custom RNS websites
  • Retrieve a large number of people page URLs (via sitemaps, crawling)
  • Grab 100 random people names and URLs from each site
  • For each name, search Google for PersonName InstitutionName
    • e.g. “Jane Doe Harvard”
  • Count what % have pages come up in the top 3

2. Results

  1. Brown 93% [VIVO] [under official domain]
  2. University of California, San Francisco 90% [Profiles] [under official domain]
  3. University of Colorado Profiles 87% [Profiles] [under official domain]
  4. Stephenson Cancer Center 87% [Pure]
  5. Mayo Clinic 85% [Pure]
  6. University of Bristol 84% [Pure] [under official domain]
  7. Royal Holloway, University of London 83% [Pure] [under official domain]
  8. University of Stirling 83% [Custom] [under official domain]
  9. King’s College London 80% [Pure] [under official domain]
  10. Oregon Health & Science University 78% [Pure]
  11. University of the Highlands and Islands 76% [Pure] [under official domain]
  12. University of Melbourne 76% [Custom] [under official domain]
  13. Lancaster University 73% [Pure] [under official domain]
  14. University of New Mexico 72% [VIVO] [under official domain]
  15. Queen’s University Belfast 71% [Pure] [under official domain]
  16. University of Strathclyde 70% [Pure] [under official domain]
  17. University of St. Andrews 70% [Pure] [under official domain]
  18. Northern Arizona University 69% [Pure]
  19. Duke 69% [VIVO] [under official domain]
  20. MD Anderson Cancer Center 68% [Pure]
  21. University of Michigan 64% [Pure] [under official domain]
  22. UT Health Science Center at San Antonio 60% [Pure] [under official domain]
  23. University of Texas at Tyler 59% [Pure] [under official domain]
  24. University of York 59% [Pure] [under official domain]
  25. The University of Texas at Austin 56.% [Pure] [under official domain]
  26. Medical College of Wisconsin 56.% [Custom] [under official domain]
  27. Boston University 55.% [Profiles] [under official domain]
  28. Northwestern University 55.% [Pure] [under official domain]
  29. University of Texas at San Antonio 51% [Pure] [under official domain]
  30. University of Dundee 50% [Pure] [under official domain]
  31. University of Minnesota 50% [Pure] [under official domain]
  32. Heriot-Watt University, Edinburgh 49% [Pure] [under official domain]
  33. UT Southwestern Medical Center 48% [Pure] [under official domain]
  34. Johns Hopkins University 48% [Pure]
  35. University of Miami 46% [Pure]
  36. University of Arizona 46% [Pure]
  37. University of Nebraska 45% [Pure]
  38. University of Utah 44% [Pure]
  39. Michigan State University 44% [Pure] [under official domain]
  40. University of Texas of the Permian Basin 44% [Pure] [under official domain]
  41. Wake Forest Baptist Medical Center 42% [Profiles] [under official domain]
  42. University of Massachusetts 41% [Profiles] [under official domain]
  43. The University of Texas at Dallas 40% [Pure] [under official domain]
  44. UT Health Northeast 40% [Pure] [under official domain]
  45. Scripps 39% [VIVO] [under official domain]
  46. Case Western Reserve University 39% [Pure]
  47. Augusta University 38% [Pure]
  48. Western Michigan University 38% [Pure]
  49. University of Texas Medical Branch at Galveston 38% [Pure] [under official domain]
  50. University of Illinois at Chicago 36% [Pure]
  51. Houston Methodist 35% [Pure] [under official domain]
  52. Albert Einstein College of Medicine 33% [Pure]
  53. University of Edinburgh 33% [Pure] [under official domain]
  54. University of Florida 32% [VIVO] [under official domain]
  55. Arizona State University 31% [Pure]
  56. University of Texas Arlington 30% [Pure] [under official domain]
  57. Stanford University 30% [Custom] [under official domain]
  58. Thomas Jefferson University 29.% [Profiles] [under official domain]
  59. The University of Texas at El Paso 28.% [Pure] [under official domain]
  60. Cornell 28.% [VIVO] [under official domain]
  61. University of Rochester 26% [Profiles] [under official domain]
  62. New York University 23% [Pure]
  63. University of Iowa 23% [Custom] [under official domain]
  64. Clemson University College 22% [Pure]
  65. Baylor College of Medicine 20% [Profiles]
  66. Indiana University School of Medicine 18% [Pure]
  67. Wayne State University 18% [Pure] [under official domain]
  68. University of Texas Health Science Center at Houston 17% [Pure] [under official domain]
  69. University of South Africa 12% [Pure]
  70. University of Idaho 10% [VIVO] [under official domain]
  71. Dartmouth 9% [VIVO] [under official domain]
  72. Griffith 8% [Custom] [under official domain]
  73. George Washington University 4% [VIVO] [under official domain]
  74. Tufts 4% [Profiles] [under official domain]
  75. US Department of Agriculture 3% [VIVO] [under official domain]
  76. University of Montana 2% [VIVO]
  77. East Carolina University 1% [VIVO] [under official domain]
  78. Texas A&M 0% [VIVO] [under official domain]
  79. Boise State 0% [VIVO]
  80. University of Hawai‘i 0% [VIVO]
  81. Idaho State 0% [VIVO]
  82. Montana State University 0% [VIVO]
  83. New Mexico State 0% [VIVO]
  84. University of Alaska Anchorage 0% [VIVO]
  85. UCLA School of Medicine 0% [Custom] [under official domain]
  86. University of Nevada, Las Vegas 0% [VIVO]
  87. University of Nevada, Reno 0% [VIVO]
  88. University of Pennsylvania 0% [VIVO] [under official domain]
  89. University of Wyoming 0% [VIVO]
  90. Virginia Commonwealth University 0% [VIVO] [under official domain]

3. Conclusions

Which software has the best real-world SEO performance?

Average scores by platform

  • Pure = 50%
  • Profiles RNS = 44%
  • Custom = 39%
  • VIVO = 15%

Average scores, by use of official vs. other domain

  • Official domain? (e.g.
    average score = 44%
  • Other domain? (e.g.
    average score = 30%

Average scores by platform, taking domain names into account (where n >= 5)

  • Pure + Institutional Domain = 53%
  • Profiles + Institutional Domain = 47%
  • Pure + other domain = 45%
  • Profiles + other domain = 35%*
  • Custom + Institutional Domain = 39%
  • VIVO + Institutional Domain = 26%
  • VIVO + other domain = 18%*

* includes some data from 2015 survey

Does getting lots of incoming links help?

It appears to. The top 10 sites have a median 560 linking root domains — one of several metrics related to incoming link diversity mentioned in the Moz Search Engine Ranking Factors 2015.

The correlation between linking root domains and search rankings holds true across our dataset:

RNS SEO 2016 root linking domains

4. How do you increase your site’s search rankings?

Read our helpful guides:

RNS SEO: How 52 research networking sites perform on Google, and what that tells us

Research networking systems (RNS) like Vivo, Profiles, SciVal, and Pure are meant to be used — but often fail to be discoverable by real users because of poor search engine optimization (SEO).

That’s why we’re releasing RNS SEO 2015, the first-ever report describing how RNS performs in terms of real-world discoverability on Google.

Continue reading

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

The 7 Keys to Maximizing Email Survey Response Rates

Lessons learned after achieving a high email survey response rate for a recent NSF Grant Study on UCSF Profiles.  Brought to you by Anirvan Chatterjee & Nooshin Latour

Your recipients don’t care about your email

The average office worker may get over 100 emails per day. Swiftly deleting or ignoring unwanted email can be the only way to stay afloat. These seven best practices will help ensure your email gets opened, read, and acted on — and not ignored or deleted.

We believe that our email marketing tactics and using customized data to drive up survey responses is widely applicable across research studies that can utilize targeted user data to increase study participation. Continue reading