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Film, Edit, Share . . . Without Leaving Your Smartphone

Mobilized - Wed, 2014-12-17 14:09

Check out this new video from the UCSF Tech Commons on how to properly use the keyboard trays in the Library’s computer labs.

This video will not be nominated for an award at the Sundance Film Festival this year, but would you believe it was filmed, edited, and distributed using just an iPhone? It was, and this post showcases the workflow and technology used to create and share a video using a single device that fits in your hand. It also follows up the previous Mobilized post, Top 5 Tips for Better Mobile Video.

Why Mobile Video?

Before we dive into all the tools and tech available for this type of project, let’s make sure we understand why we would want to use our mobile device to produce a video. Here are just a few scenarios where you may want to take out your phone and start recording (and then editing):

  • Interview a colleague to promote a new service in your school or department
  • Document a conference or professional development event
  • Create a video to use on your website or in your CLE course
  • The digital video equipment offered through the UCSF Library is not available
  • You have a limited budget and little digital video experience

Notice what these different videos have in common? They all involve short videos that require minimal editing and have a clear objective.

Now that we have thought about the Why, let’s talk about the How. The keyboard tray video was filmed, edited, and shared using just one device, but I combined a number of apps and equipment to accomplish this, including:

  1. iPhone 6 camera to record video
  2. Slow-Mo setting on the iPhone 6 camera
  3. Voice Memos app on the iPhone 6 to record audio
  4. iMovie iPhone app to edit the footage
  5. YouTube to upload and distribute the video
  6. Tripod for filming

Here is a summary of my workflow used to create the video:


Just because I used a mobile device to create this video, it does not mean I could skip outlining the video, that is, storyboarding! The first thing I did was outline what I wanted to cover in the video and identified the clips, audio, and images that I needed to capture. I turned this into a list of video clips and pictures (a shot list) that I could quickly check off while filming.

This is what my storyboard looked like:


Armed with my storyboard and shot list, I started filming the clips in sequence using the iPhone 6 camera. You may notice that certain audio in the video carries over from one clip to the next. This was done by recording audio in the Voice Memo app, which I later imported in the iMovie video project during editing.

An extremely helpful piece of equipment for this project was the tripod. I recently purchased the Kooteck Tripod for Smartphones from Amazon.com for $12.99. This resulted in steadier, more professional-looking shots, especially when shooting in slow motion. I also used the iPhone’s camera to take a few pictures that I used for b-roll, also known as alternative footage.

Oh, and don’t forget to hold your phone horizontally while filming! There are very good reasons to avoid vertical videos. Learn more about Vertical Video Syndrome.


I purchased the iPhone iMovie app for $4.99 to edit the video. I chose iMovie, because I use the desktop application frequently and was interested in how the video editing experience differed on a 4.7” screen. Of course, there are many other free and paid video-editing apps to choose from in both the Android and Apple iOS markets. If there is a specific app that you like to use, please let us know in the comment section below!

Using the iMovie app, I added titles, transitions, and a jingle to enhance the video. The jingles that come with the iMovie app are royalty free, but there are fewer options in the mobile app than what you get in the desktop version of iMovie. Even though my audio options were limited, I was still able to use sound to cover up some awkward silences and improve the overall quality of the video.

Here is a screenshot from my iMovie project showing the video and audio tracks:

When I was finished, I exported the final video out of iMovie to the iPhone camera roll. The size of the 36-second video was just 7MB (not bad)!


Now for the easy part — sharing your masterpiece with colleagues! I uploaded the final video directly from my iPhone to YouTube, which only took a few moments. I added a description as well as important metadata or tags to help people find the video when searching. I uploaded the video to YouTube because YouTube integrates well with the platform used for this blog, making it easier to embed my final video in the post you are reading now.

I can now share my video in an email, via the UCSF CLE, or on my department website! Make sure to check out UCSF’s media distribution system, Media@UCSF, for sharing UCSF-related videos. You can also read more about Media@UCSF on the Convergence blog.

That’s a Wrap

And that is one example of how you can film, edit, and share a video using only your mobile device! This video took no more than an hour to create from start to finish and was done using only the iPhone. No work was done using a laptop or desktop computer and no cables were needed!

Do you need assistance creating your own video using a mobile device? Stop by the UCSF Library’s Tech Commons or attend a Tech Clinic with the Learning Technologies Group for tips and tricks for creating your own video. Remember, you do not need an iPhone 6 to create an effective video — you just need to know the tools, apps, and resources available, and start filming!

Check out the resources below for creating videos using mobile devices:

Lastly, thank you UCSF Library staff member, Ben Stever for your patience and cooperation during the filming of this video!

Categories: Mobilized

Holiday Wishes from UCSF Archives!

Brought to Light Blog - Wed, 2014-12-17 12:20

Dear supporters and friends of UCSF Archives & Special Collections!

We would like to express our gratitude to all of you for your help in building our historical collections through donations of rare books, personal papers, and unique artifacts. Thank you for taking the time to read how UCSF Archives preserves the history of UCSF.
Over the past several years we have been providing archival documents, photographs and film footage to enrich the celebration of UCSF’s 150th Anniversary. This year we inaugurated archives lecture series and launched a Twitter account to share historical tidbits, provide updates on events, acquisitions and our diverse projects. Currently the archives team is working on several exhibits commemorating UCSF’s achievements that will be opened in 2015.

Looking forward to serving you in the New Year!

Categories: Brought to Light

New UCSF Library Subject Guide on Data Sharing and Data Management

In Plain Sight - Wed, 2014-12-17 10:08












Funding bodies increasingly require grant-holders to develop and implement Data Management and Sharing Plans (DMPs). Plans typically state what data will be created and how, and outline the plans for sharing and preservation, noting what is appropriate given the nature of the data and any restrictions that may need to be applied.

The Library has created a new Subject Guide that provides an introduction to data sharing and data management, with an emphasis on those issues affecting those of you submitting grant applications to the National Institutes of Health (NIH). New Library-supported tools such as DataShare and DMPTool are highlighted.

Categories: In Plain Sight

UCSF Clock Tower

Brought to Light Blog - Thu, 2014-12-11 12:04

Millberry Union Clock Tower, 2014

Have you ever noticed the large transparent clock on the exterior of Millberry Union? It looks like this:

I walk past it often without giving it a second thought, but the clock tower has quite an interesting history.

Often referred to now as the “Founders’ Clock,” it is also known as the “Toland Clock Tower” and “Seth Thomas Clock.” You may also have seen photographs of the Old Medical School building from time to time, with a large clock atop the center of the building– the same clock as Millberry’s clock.

One of our rotating banner images here on Brought to Light depicts the old Medical Building, including the Seth Thomas Clock, through the lens of well-known photographer Ansel Adams. It’s a slice of this photograph:

Ansel Adams, Clock Tower of old Affiliated Colleges building, with new structures in fog, August 1964

The above building was the College of Medicine, and the first building to have been erected on the Parnassus campus in 1897. Seth Thomas was a well-known clockmaker in Connecticut in the early and mid 19th century. The clock was brought to San Francisco via ship that traveled around Cape Horn, South America to be a crown jewel in the Affiliated Colleges campus. The image, taken in 1964, shows the old College of Medicine building surrounded by the more modern campus buildings of today in the background and on the left. When the old College of Medicine building was torn down in 1967, a group of “friends of the clock”, led by Alison Saunders, MD and assisted by Meyer Schindler, MD ’38, formed to ensure it’s safekeeping until it could be moved to a new location on campus. “We have salvaged the granite pillars and blocks as well as the clock from the old building that was a landmark on Parnassus Heights . . . ,” Dr. Alison Saunders declared in 1969 as chair of the UCSF Campus Court Development Commission.

The process to find the famous clock a new home took 14 years. Finally, in 1982 the inner-workings of the clock were reinstalled on Millberry Union, 500 Parnassus Ave, where it lives today.

Founders Clock, Millberry Union, circa 1982

Next time you’re walking around the Parnassus campus, take a closer look at the historic clock. It is a work of art worthy of our attention.

The inscription reads: “Carried by ship around Cape Horn, this Seth Thomas Clock was installed on the Medical School of the Affiliated Colleges in 1897. Surviving the 1906 earthquake, it served the University and community for 70 years. Members of the UCSF family have made possible its restoration as a campus landmark.”

Check out this article that details the historical inspiration for a new clock, “Saunder’s Clock,” in the Mission Hall courtyard of the UCSF Mission Bay campus.

Categories: Brought to Light

Exploring the Archives for 150: Dr. Mary Olney’s Summer Camp for Children with Diabetes

Brought to Light Blog - Tue, 2014-12-09 09:02

In preparation for UCSF’s 150th anniversary celebration exhibits, we’ve been doing a bit of exploring in the vaults. For the next several months, I’ll be posting some of the treasures we’ve discovered!

In 1938, UCSF pediatrician Mary B. Olney founded the first wilderness camp in California for children with diabetes. Unlike many of her contemporaries, Dr. Olney believed that diabetic children could live active, healthy lives through proper disease management. Dr. Olney, known as “Doc” to her young patients, provided a fun, supportive space and encouraged campers to take control of their health. Bearskin Meadow Camp is still active today thanks in large part to the tradition of care and empowerment fostered by Olney.

Dr. Mary Olney on a hike, ca. 1940. MSS 98-64, box 1, folder 6

Dr. Olney graduated from UCSF in 1932. She completed her training in pediatrics at San Francisco General Hospital and was later appointed Clinical Professor of Pediatrics at UCSF. At the time of her death in 1993, Olney had served the UCSF community for over fifty years.

A camp postcard filled in by Dr. Mary Olney while at Bearskin Meadow. It is addressed to her father, 1961. MSS 98-64, box 1, folder 27

Olney’s first group of campers attended a two-week session at Los Posados in Napa County. The camp eventually developed into Bearskin Meadow, a permanent campsite located near Kings Canyon National Park. The camp welcomed boys and girls and provided coeducational activities. Diabetes management instruction focused on diet, exercise, and proper insulin administration.

Dr. Mary Olney teaching a nutrition class for campers. MSS 98-64, box 1, folder 6

Camp staff performing urinalyses. Photograph with original caption, perhaps from a deconstructed scrapbook. MSS 98-64, box 2, folder 45

Olney and the counselors, many of whom were medical students, taught a holistic system of care that campers could take home with them.

Camp staff and counselors, ca. 1941. MSS 98-64, box 1, folder 34

Alongside nutrition classes and medication instruction, campers took nature hikes, learned to swim, played sports, and sang campfire songs. As Olney later noted in a 1988 interview in the UCSF Alumni Faculty Association Bulletin, this physically robust approach to diabetes management differed dramatically from older systems. Olney remembered that when campers first arrived, they often “didn’t know they could do hiking because the old way of treating diabetes was to let the child go from school to home and sit in a chair until suppertime and then go to bed.”

Camp announcement noting the different activities of a typical camp day, 1962. MSS 98-64, box 2, folder 77

UCSF continues to honor and support Olney’s work through the Mary B. Olney MD / KAK Chair in Pediatric Diabetes and Clinical Research. In the archives, we house the Mary B. Olney papers, MSS 98-64. The collection includes camp photographs, correspondence, meal plans, and publicity and fundraising material. It also contains records relating to the Diabetic Youth Foundation, an organization created by Olney and her longtime partner Dr. Ellen Simpson to help administer the camp and other services.

The cover image of Bear Facts, vol II, no. 6, a publication created by campers and counselors at Bearskin Meadow Camp. The Mary B. Olney collection includes numerous different issues of Bear Facts. MSS 98-64, box addition 3, folder 4

To view more items from the Mary B. Olney papers, visit our digital collections!

Categories: Brought to Light

Lecture now online: Shimkin’s “Lost Colony” (1947-1953)

Brought to Light Blog - Thu, 2014-12-04 09:04

The lecture Shimkin’s “Lost Colony” (1947-1953): Early Interdisciplinary Cancer Research at UCSF presented by Michael Thaler, MD, MA last month on October 13th is now available online free via the Internet Archive.

(It seems that Polina’s microphone wasn’t turned on; just be patient, the sound is fine for Dr. Thaler’s presentation.)

The Laboratory of Experimental Oncology (LEO) was the brain child of Michael B. Shimkin, a career U.S. Public Health Service physician and cancer research at the National Cancer Institute. LEO was established in 1947 at Laguna Honda Hospital at Laguna Honda Hospital, jointly administered by the NCI and UCSF. Speaker Michael Thaler, MD, MA explains how Shimkin created one of the first combined interdisciplinary clinical and basic science research units embedded in a medical school. In this setting, Shimkin introduced the patient release form and was instrumental in the establishment of universal guidelines for the ethical conduct of experiments with human subjects.

Dr. Thaler spoke as part of our ongoing UCSF Archives & Special Collections Lecture Series which serves to introduce a wider community to our holdings, provide an opportunity for researchers to discuss how they use this material, and celebrate clinicians, scientists, and health care professionals who have donated their papers to the archives.

Next, we will welcome Mark Honigsbaum, PhD to discuss Karl F. Meyer: California’s Forgotten Microbe Hunter on Friday, December 5th at noon in the Library’s Lange Room. Please join us!

Categories: Brought to Light

RefWorks and Mac OS Yosemite (10.10)

In Plain Sight - Mon, 2014-12-01 12:16

This information is from the University of Virginia Library:

“If your new Mac has the Yosemite operating system, when you download WNC 4 be sure to select WNC4 version 4.4.1225 as this is compatible with OSX 10.10.  This is the second link listed as an option for download.  If you have upgraded your older Mac to Yosemite, you will need to turn on your Java application before downloading WNC4.”

Categories: In Plain Sight

World AIDS Day

Brought to Light Blog - Mon, 2014-12-01 09:00

AIDS Research License Plate Program application form, UCSF Center for AIDS Prevention Studies (CAPS) records

UCSF Archives continues to collect and preserve AIDS History materials. Here is a list of recently cataloged collections that can be viewed in the reading room:
AR 2005-15, UCSF Center for AIDS Prevention Studies (CAPS) records, 1984-2004
AR 2007-14, UCSF AIDS Health Project records, 1983-2003
MSS 2001-04, Sally Hughes AIDS research collection, 1981-1997
MSS 96-32, Brooks Linton ephemera collection, 1983-1995

Categories: Brought to Light

Thanksgiving recipes from Doctor’s Wives Association

Brought to Light Blog - Wed, 2014-11-26 09:00

The holidays are almost here… Are you still searching for a perfect recipe to amaze your guests and share with the family? Look no further! “Kitchen Consultations,” a cookbook which was put together in 1950 by the University of California Doctor’s Wives Association – a group of “health-minded, vitamin conscious women who used these recipes in their own homes.” This organization traces its origins to 1917 when its first members met and adopted the name “Ladies of the Medical Faculty of UC.” In 1925 the name was changed to “Doctors’ Wives Association of U.C.,” but the goals remained the same – working for the benefit of the hospital and especially pediatric wards. Later the major fundraising efforts were directed to Dr. Mary Olney’s Diabetic Youth Camp as well as amenities for patients, loan fund for students and the Founder’s Clock restoration.

“Kitchen Consultations,” a cookbook compiled in 1950 by the University of California Doctor’s Wives Association

The exquisite artwork in the book was done by Ralph Sweet, professor of Medical Arts and Illustrations at UCSF Medical School.

Here is a selection of recipes for a four course dinner…

Golden Gate Soup recipe by Mrs. Seymour Farber

Stuffed Meat Rolls by Mrs. Ralph Sweet

Corn Bread Turkey Dressing by Mrs. Donald Smith

String-Bean Casserole by Mrs. Clark Johnson

Pecan Pie recipe by Mrs. Thomas Fullenlove

Happy Thanksgiving and best wishes from the UCSF Archives team!

“Kitchen Consultations” cookbook is part of the Faculty Wives, University of California, San Francisco Records, 1948-87 and can be consulted in the archives reading room.

Categories: Brought to Light

Using Papers 3 (Mekentosj) for Collaboration: Papers Online

In Plain Sight - Mon, 2014-11-24 15:00

Though Mekentosj’s Papers application can be considered a reference manager, allowing you to cite research sources and format a bibliography, its greatest strength is its use as an online system to help you effectively manage research collections.

Papers 3 for Mac, Windows and iOS now includes a new collaborative feature, Papers Online. Papers Online introduces two features: Shared Collections and the Reading List. Shared Collections are collections of papers that are stored online and can be accessed and edited by multiple people. Only metadata are shared, but Papers will allow you to download and save PDFs for the documents as it usually does. The reading list gives you several new ways to more easily get articles in and out of Papers and keep track of what you are currently researching.

For more general information about Papers 3 view this online video.




Categories: In Plain Sight

Course Design Tips

Convergence - Fri, 2014-11-21 10:05

Managing an online course can range from straightforward to complicated, and can become overwhelming at times. It is also uncommon to receive a manual when you are tasked with developing an online course. Not to worry – help is here! As learning technologies staff, we live and breathe the CLE!

With a little planning and development, we can build the foundation of a great CLE course. Below are just a few CLE course design tips and resources we identify as valuable. We hope these generate conversation and new ideas within your course, school, and department.


Design for mobile

The number one tip for this blog post is… design CLE courses for students using both laptops and mobile devices! Data shows students are accessing CLE courses using mobile devices more and more. This means we need to rethink the way we design courses in the CLE, specifically how we format images and text.

The CLE 2014 Refresh brought responsive design to the CLE. The CLE now responds and displays according to the device being used by the student. This means no more small, unreadable text when accessing the CLE from a mobile device such as an iPhone or Galaxy.

Here is a practical tip for improving the learning experience for students accessing the CLE from either a mobile device or a desktop computer – remove tables from CLE courses that are being used to format text and images. Replace these tables with images and text wraps that are designed to properly respond to students’ devices. Sound complicated? Maybe a little, but not to worry, we are simply replacing tables with images and text to create better designed, more user-friendly CLE courses!

For the purposes of this example, we will add a Label to a course to display an image and a summary of the week’s learning as seen below.

In the past we would have used a table to keep the image and text aligned in the label. This works well when viewed on a laptop or desktop computer, but once the content is accessed from a mobile device, the text does not display correctly on the smaller screen (in other words, the text does not “respond”). When tables are used for formatting text and images, students using mobile devices may experience cumbersome horizontal scroll bars (see images below), text that runs off the screen, and images that do not display correctly.

So how do we fix this? Just remove the tables that are used to format images and text in CLE courses and replace these with image wraps. Below is a side-by-side comparison of the two design workflows, as well as screenshots of how the two will display on a mobile device:

And here is a comparison of how both will display on a mobile device:

Here is how to apply an image wrap in a Label. Add a Label to a CLE course and insert text and an image into the text editor. While adding the image, navigate to the Appearance tab in the Insert/edit image pop-up (shown in the image to the right). From the Alignment drop down menu, choose Left to align the image to the left of the text (there are other alignment options available). From the Horizontal space field (how much space is added between the image and text), I entered 10 (pixels) for this example, which worked well. Click Update to continue.

That is it! You can now replicate this design workflow in other labels in your CLE course – creating a consistent learning experience for students. Questions? Comments? Post a comment below and let us know if students in your course are using mobile devices to access the CLE and if you have design tips of your own!

Block Management

The second course design tip is better Block Management. Blocks are items that can be added to the left or right column of any CLE course. There are a number of different types of Blocks in the CLE and some may already be used in your course.

The first step to good Block management is understanding the different types of Blocks. Take a look at the Standard Blocks via Moodle Docs and explore the different types of Blocks available in the CLE (with editing turned on!).

The next step is to add only the Blocks that add value to the online experience. If a Block is not used, or has little value, consider removing it from the CLE course to conserve space for learning. Spend 10-15 minutes before each semester reviewing your Blocks, as well as considering how different types of Blocks can be used to improve the online learning experience for both students AND faculty.

CLE courses are divided into three columns and Blocks are typically located in the left and/or right columns. The middle column is where the course content is displayed and where students spend the majority of their time learning while in the course. To maximize the amount of real estate in this middle column, consider moving all of your Blocks to the left column. Once all of the Blocks have been moved from the right column to the left, the middle column becomes wider, extending to the end of the right column and providing more space for learning. See the images below for a visual comparison of the impact of better Block management:

Have questions about managing Blocks? Visit the CLE Knowledge Base for more information!


So you are probably thinking, “this is useful information, but I need CLE course design support now!” Not to worry, below is a list of resources that we find helpful when creating CLE courses:

find examples of well-designed online courses

The best to way to be motivated and inspired to improve your CLE course is took look at examples of other well-designed online courses. These courses do not need to be in the CLE, or even Moodle courses necessarily. By getting a better understanding of the successes that other educators have had with online course design, we can create better online learning environments for students. Below are resources with good examples of online course design:

Attend a Tech Clinic

Need one-on-one support? Attend a Tech Clinic held on the second and forth Friday of every month. We also offer a CLE Basics training at the start of each Clinic that we highly recommend new faculty and staff attend. Register today!

Create a CLE Test Course

Not quite ready to test the course design tips in an active CLE course, but want to get a head start on next semester? Request a CLE test course where you can test design workflows and tryout new CLE activities.

LTG consultation using WebEx

Whether you are a rookie or a veteran of the CLE, questions come up! The Learning Technologies Group can setup a WebEx session to help troubleshoot CLE related issues and assist in course design suggestions – all from the comfort of you own office. Contact the Learning Technologies Group to schedule a CLE WebEx consultation.

Have fun designing your CLE course and please share you successes and challenges in the comment section below!

Image Credits:

Blocks” designed by Lukasz M. Pogoda from the Noun Project.
Responsive-Design” designed by Pham Thi Dieu Linh from the Noun Project.
Graphic-Design” designed by Anna Weiss from the Noun Project.

Categories: Convergence

Through the Eyes of an Intern

Brought to Light Blog - Thu, 2014-11-20 15:04

Hi everyone, my name is Armani Fontanilla and I am an undergraduate student at the University of San Francisco interning at the UCSF Archives & Special Collections.

At the archives, I am currently tasked with the processing of small box collections, or the creation of box level inventories and the digitizing, and creation of, metadata for the archives that have yet to be placed into the virtual catalog. Other projects that I am potentially tasked with are research for the upcoming 150th Anniversary of UCSF on the level of researching stories, scanning images, and looking for documents, as well as helping with the vast inventory of the Medical Artifacts collection.

It’s restricted for a reason. We can’t reveal why. All you need to know is Maggie has the really cool “restricted” stamp. It’s actually really cool.

And wow is our inventory big… Get it? Because the texts are big?

Even though the potential projects are only potential projects, my senior co-workers, Maggie and Kelsi have both taught me a lot in the projects that I am currently working on. For example, Kelsi has taught me about her work with the Medical Artifacts collection: How the UCSF catalogs have changed from one form to another, and that cross-referencing catalogs with each new edition that has come through the library archives since 1864, one also has to decipher the writings and annotations of previous archivists, as well as come up with new ways to reorganize the collections in our possession.

Maggie, on the other hand, has taught me how to do the projects that I am currently doing, as opposed to the potential projects that Kelsi lets me shadow every so often. She has taught me proper labeling procedure, and storage techniques, as well as projects that mirror the one that Kelsi is currently doing, which would be creating catalogs for documents in storage.

Cataloging kind of like this, but more modern.

Finally, the first project (that I am still working on when I’m not being taught by Maggie or Kelsi, is the creation of a digital inventory of UCSF affiliates and members. Fortunately, most of the physical inventory is in English, and it is all on-site. Unfortunately, the physical inventory itself is not backed up – folders that are not archival standard need to be replaced, labels need to be printed out because of the inconsistent handwriting of previous archivists (and this intern’s), and more files need to be created for the ever expanding role of UCSF affiliated persons who are recognized in the news worldwide – from China, to America, to Brazil, to the Philippines, UCSF’s impact on the world is growing. And my first, and current job, is to help sort the files so that we can keep track of them for people to use and peruse in the future.

Before this data can hit the internet, I need make sure they’re all in order.

Within these jumbled folders, however, lie treasures that I am so excited to find. While often the files just contain one or two articles, some contain as many as ten plus! And these articles are often varied – they come in the form of obituaries, photocopied documents, magazine clippings, newspaper articles, biographies, and more! But instead of letting me describe them, let me show you some examples.

A button with 1989 Nobel Prize Winners Michael Bishop and Harold Varmus.

Brown, Leatha. School of Nursing, Class of 1928.

Holt A. Cheng, 1904. He was the first Chinese to be licensed to practice medicine in California after graduating from the College of Physicians and Surgeons in San Francisco. After returning to China, he established the Guang Hua Medical Society, the first medical college of western medicine established by the Chinese, for the Chinese, and the first medical school to accept female applicants.

And finally, the UCSF archives are not only home to just Western schools of thought in medicine, but include Eastern Thought as well. On site and in a state-of-the art archival room, various Eastern texts in Chinese and Japanese are stored, either purchased by the Head Archivist, donated to UCSF, or willed by their owners.

Chinese medical texts in the archival room.

Japanese medical texts.


Armani Fontanilla

Armani is currently a senior majoring in History with an emphasis on European and Asian Studies in the University of San Francisco (USF) public history program. After he graduates, he hopes to be able to earn a teaching position at his old high school, Bellarmine College Preparatory, and eventually pursue a Masters. In choosing the UCSF archives through the USF internship program, he hopes to not only practice skills that can only be found through working at an established institution but to also enhance his ability to do archival work and explore history of Western medicine at the archives.


Categories: Brought to Light

Reporting on the CLE Refresh Survey

Convergence - Tue, 2014-11-18 08:46

On August 2, 2014, the CLE underwent a major refresh with the installation of a completely new user interface. While this update also included a number of important performance and course-building enhancements, the crucial new feature — one that impacts all CLE users — was the new interface. Finally, we were able to fulfill easily the most requested CLE feature for the past few years — make it so that the CLE works better on smartphones and tablets. The new interface is now mobile-friendly, and incorporates responsive web design principles, which means it seamlessly conforms to the screen size of the device viewing it, be it a 27-inch desktop monitor, iPad Mini, iPhone or Android smartphone. Along with the refresh, we also released a short survey on August 2 to start gathering some feedback about the changes. We received seventy-three submissions through August. In this blog post, we report on some of the survey results and some directions for the future.

The survey asked everyone to grade the CLE refresh. Over 71% gave the refresh a C or better, and half of all respondents gave a grade of B or better. Here is a sampling of some of the comments:

This look is much clearer, cleaner and user friendly!

The graphics/skin of the interface is clean. All functions appear to be intact. No major re-learning required for average user.


It is clean looking and more up to date.

I like the clean look. There are less extras that take your attention away from the content. The colors are softer and cleaner as well.

Looks less cluttered which helps with visual appearance.

Much more mobile friendly.

It looks more updated and seems to be less buggy. Also, it seems to work better with Chrome than the old version.

Given that this refresh brought some major changes, this was a good start. But while most gave the new CLE a passing grade or better, there were also some who felt that the new CLE look and feel didn’t quite past muster:

I do not like the mobile version nor do I like the new homepage, too sparse and it doesn’t highlight my interest like the login button.

There is too much blank space for each menu. That has made it a bit too bulky and can’t fit all the necessary information without scrolling.

I usually use CLE to get to UCSF’s library resources like Pubmed, and it has been difficult for me to figure out how to navigate to this page.

There needs to be a drop down menu for lecture capture. Having all the classes on the same screen with the calendar is too cluttered and overwhelming.

The calendar does not fit, I needed to drag every time I need to move to the next week for see Friday.

The CLE team has already incorporated some of this feedback into a recent update. Some felt that the blocks (e.g., Navigation, Administration) that appear in CLE courses on the left and/or right were taking up too much space. We were able to reduce the block footprint so that there is now more room in the center area where the main course content resides. Other survey comments will be reflected in upcoming updates, including:

  • Reduce the block footprint even more so that the main course content takes precedence.
  • Make sure that on smaller screen sizes, the blocks do not take up valuable space so that important course content, such as the Ilios calendar, doesn’t get squished.
  • Making the Log In link consistently visible at the top for all screen sizes. Currently, the Log In link is no longer visible on small screens — it gets hidden inside the menu icon when the screen size gets small, making it difficult to locate.
  • Add a Maximize this page button on all CLE pages that will allow the main content area to immediately fill the entire screen.

Future updates to the underlying Moodle learning management system that powers the CLE will also bring new features, such as much improved responsive behavior for all screen sizes and a user menu in the header that provides quick access to personal pages. Other survey comments suggested what would essentially be entirely new features, such as a way to provide quicker and less cluttered access to lecture capture recordings.

We invite you to continue providing feedback — the good, bad and ugly. The August 2014 refresh placed the CLE on a solid foundation from which to grow and improve. Your comments, feedback, and feature requests will be absolutely vital in this process. We plan to release new short surveys over the coming months. We also invite you to send any and all feedback to the Learning Technologies Group.

Categories: Convergence

EndNote Update X7.2 Provides More Features for Collaboration

In Plain Sight - Thu, 2014-11-13 12:13

EndNote has released it’s latest update, X7.2. The major new feature is the ability to use an EndNote online account to share a library with up to 14 collaborators. You’re also given unlimited online storage so you can store and share as many files as you need.

On opening EndNote X7 you’ll be prompted to update to X7.2.

With X7.2 you can:

  • share a library with anyone who’s using EndNote X7 (with up to 14 people)
  • sync attachments, notes, and annotations in real-time for collaboration
  • share your entire EndNote library, including references, PDFs, and annotations
  • share just groups
  • add to, annotate and use the library – at the same time as others

For more information:









Categories: In Plain Sight

UCSF Archives Lecture: Karl F. Meyer, California’s Forgotten Microbe Hunter, December 5, 2014

Brought to Light Blog - Thu, 2014-11-13 09:31

Join us on Friday, December 5th as Mark Honigsbaum, PhD, gives a lecture in a series launched by UCSF Archives & Special Collections.

Date: Friday, December 5th, 2014
Time: 12 pm-1:20 pm
Location: Lange Room, UCSF Library, 530 Parnassus, 5th floor
This lecture is free and open to the public. Light refreshments provided.
Please RSVP to reserve a seat.

In the 1930s California’s rapid population growth and the incursion of agricultural settlers into valleys and deserts teeming with exotic pathogens resulted in outbreaks of ‘new’ infectious diseases. To divine the cause of these outbreaks and trace the epidemics to their source, health officials turned to San Francisco’s premier ‘microbe hunter,’ Karl Friedrich Meyer.

Karl F. Meyer in his office.

All but forgotten today, Meyer was once a nationwide figure renowned for his feats of disease detection. As director of the George Williams Hooper Foundation for Medical Research at UCSF in the 1920s, Meyer – a Swiss-born veterinarian and bacteriologist – spearheaded investigations into botulism, mussel poisoning, and brucellosis. By the 1930s he focused increasingly on parasitic diseases of birds and other animals.

These included ‘parrot fever,’ a deadly disease caused by a bacterium in parakeet droppings, and ‘staggers’ (equine encephalitis), a viral disease of horses spread by mosquitoes that bred in irrigation ditches. Most famously, they also included outbreaks of ‘sylvatic’ plague along the California-Oregon border – outbreaks that Meyer traced to migrations of squirrels and other flea-infested rodents. What linked these outbreaks is that, one way or another, they were all ‘man-made’ – the result of human interference with animal ecologies.

Drawing on Meyer’s papers at the UCSF and Bancroft libraries, this talk reviews Meyer’s feats of microbial detection and his pioneering investigations of disease ecology. Dr. Honigsbaum views Meyer as an important bridge figure in mid-20th century medical research who sought to link microbial behavior to broader environmental and social factors that impact host-pathogen interactions and the mechanisms of disease control.

Mark Honigsbaum

Mark Honigsbaum, PhD, is a medical historian and journalist with wide-ranging interests encompassing health, science, technology and contemporary culture. A specialist in the history of epidemics and pandemics, he is the author of four books, including The Fever Trail: In Search of the Cure for Malaria and A History of the Great Influenza Pandemics: Death, Panic, and Hysteria, 1830-1920. He is currently working on a history disease ecology as a Wellcome Research Fellow at Queen Mary University of London.

About the UCSF Archives & Special Collections Lecture Series

UCSF Archives & Special Collections launched this lecture series to introduce a wider community to treasures and collections from its holdings, to provide an opportunity for researchers to discuss how they use this material, and to celebrate clinicians, scientists, and health care professionals who donated their papers to the archives.

Categories: Brought to Light

Got Videos? Media Sharing Now Available on the CLE!

Convergence - Thu, 2014-11-13 08:54

For some time now, UCSF has been in need of a place to store and manage video files to be shared across the University and for the public. Although Vimeo has been a resource on campus, the uploading process has traditionally not been available to all UCSF users, such as students. The time is finally here! The UCSF Library is now pleased to present a fully-functional system available to all staff, students, and faculty, called Media@UCSF.

Media@UCSF is an online video-hosting platform powered by Kaltura and provides the UCSF community with a centralized system for managing and distributing digital video content. Media@UCSF is fully integrated into the CLE, providing instructors and students with the tools to create, edit, and share videos in a course.

Anyone at UCSF can start using Media@UCSF now by logging into media.ucsf.edu. This blog post, however, will focus on the CLE integration.

Check out this support document to learn more about the different components that integrate with the UCSF CLE:

The Learning Technologies Group has also created documentation on the following topics:

  • Uploading Media
  • Sharing Media in the CLE
  • Inserting and Grading a Media Assignment

Find these step by step instructions in our new Support Center.

To learn more, join us tomorrow at the Collaboration Roundtable hosted by the Library’s Learning Technologies Group. This month’s Roundtable will focus solely on Media@UCSF and takes place from 12 – 1pm in CL-215 in the Parnassus Library. Register to let us know your coming and feel free to bring your lunch while you learn about this new tool.

Image Credits: dsathiyarajErin Standley

Categories: Convergence

Commemorating UCSF Dental Alumni WWI Veterans

Brought to Light Blog - Mon, 2014-11-10 08:57

In honor of Veterans’ Day this year, we bring you a scrapbook from our collection, titled Dental College Alumni Serving in the First World War, 1917-1919. The scrapbook is filled with letters written to Dr. Guy S. Millberry by both former and on-leave students during their military service. Millberry began working at UCSF in 1906, was appointed Professor in 1910, and became Dean of Dentistry in 1914– a role he continued in for twenty-five years.

The collected letters were written from a variety of places– Camp Greenleaf, GA; Camp Fremont, CA; Vancouver, WA; Royat, France; Oakland, CA; Camp MacArthur, TX; San Pedro, CA; Camp Lewis, WA; Khabarovsk, Siberia; New York, NY; Fort D.A. Russell, WY; Camp Greene, NC; Camp Shelby, MS; Camp Lee, VA; La Ferte, France. They were sent from forts, camps, ships, submarines, and hospitals. Most of the the letters are handwritten, a few are typewritten.

Dental College Alumni Serving in the First World War, 1917-1919 scrapbook


The soldiers ask Dr. Millberry for letters of recommendation, job advice, proof of graduation, if their leave of absence will be honored or extended to allow them return to school after the war ends, and give updates on their lives. One soldier, who wrote on September 21, 1918, included a copy his records detailing the dental work he did in one week.

Dental College Alumni Serving in the First World War, 1917-1919 scrapbook

A graduate of the 1917 UC College of Dentistry class, Edwin Busse, wrote a letter on October 18, 1918 from his station in Paimboeuf, France that included several photographs (the letter is transcribed in full at the end of this post). Busse is pictured in the 1917 Blue and Gold UC yearbook as a member of the Psi Omega dentistry fraternity. Below, a photograph of the Arch de Triumph in Paris, France. The caption reads: “Note how French have protected statue on right with sandbags.”

Dental College Alumni Serving in the First World War, 1917-1919 scrapbook

Included with same letter, a photograph of a “portable dental outfit.”

Dental College Alumni Serving in the First World War, 1917-1919 scrapbook

As well as a photograph of a “dental office at Paimboeuf.”

Dental College Alumni Serving in the First World War, 1917-1919 scrapbook


Clark R. Giles received his Degree of Doctor of Dental Surgery from UC in 1914 and had been an instructor in Prosthetic Dentistry here before serving in World War I. He wrote a detailed letter to Millbery on on October 7, 1918 from Royat, France describing the work that goes on at Base Hospital 30, the war, his recent leave, and even mentions Busse.


Dental College Alumni Serving in the First World War, 1917-1919 scrapbook

Royat France
Oct 7, 1918

My dear Dr. Millberry:

I have been a long time in writing to you but rest assured it is not because I have not thought many times of you and of the University.

We are located in Royat near Claremont-Ferrand a city of 60 thousand. We have the hospital well established in 17 or 18 summer hotels and at present have a little more than 1700 patients and within a few months expect to be able to care for 3 thousand if necessary.

Our department is very comfortably (not lavishly, naturally) equipped and just at present we are five dentists and six assistants. However we expect to lose our extra help ere long but in all probabilities they will be replaced by men from incoming organizations. We are kept very busy for example last month we saw some 650 patients and we try to have each man who comes in, go out with his mouth in a completed condition. We naturally have a great amount of routine work to do but mixed with it are also numerous very interesting wound and fracture cases from which we learn a great deal in the surgical and fracture line. All cases involving facial or other structures than the jaws or teeth are as you probably know handled in conjunction with the surgical department.

Click through to read the rest of the letter written by Giles followed by the letter from Busse that included the photographs, written to Millberry a week later than Giles’, also from France. 

One case it has been my good fortune to handle was of two huge cysts involving one, almost the entire body of the sup. maxilla, and the other leaving just a shell of the mandibula running back under the first molars of each side. They were the largest things of the sort I have ever seen but at present new tissue is building very nicely and I hope for a nice final result in time.

We at most times have one or two fractured mandibules on hand so I feel that if when I return to San Francisco and see a fractured jaw come in I won’t be very badly excited by it. I feel that I learned a considerable number of points about such cases from Dr. Winters clinics in the two weeks we spent with him in New York. But must add that after visiting the colleges in New York I felt proud to have received my training in the U. of C. and then and there decided that you do not have to “go fast” to get the good things of the profession.

Have only met one of our men since I have been over here (now nearly six months) Maurice Gloyier, who is with an ammunition train that is in a camp nearby just at present. Have rec’d letters from Edwin Busse but do not know of the whereabouts of any of the others.

I have just returned from my first “leave” having had 7 days exclusive of travelling time. I went to Marseille, Nice, Nîmes, Monaco, Monte Carlo, Menton, crossed the Italian border and came back by way of Lyon. I surely had a wonderfully interesting and beautiful trip. Would like to have gone to Paris but at present that is “out of bounds” but hope to get there later by some method or other.

Things are surely going beautifully on the “Front” of late and from the declaration of day before yesterday guess we must have the old Kaiser standing first on one foot than the other.

Well we anxiously await the results of this huge diplomatic week and hope always for peace.

If you are not too busy, and I have never seen you too busy to take on some new task, I would be more than pleased to hear from you.


Clark R. Giles
Base Hospital 30


Dental College Alumni Serving in the First World War, 1917-1919 scrapbook

Paimbeouf, France
October 18,1918

Dear Doctor;

I am enclosing a few pictures which may be of some interest to you and for which you asked some time ago.

Of course over here the problem is films and paper. So far I have not been able to get any that fit my camera, and as you may see, those I brought from home have suffered from age and have made spotted prints.

The work over here continues to be far from interesting. This is due no doubt to the very limited means we have of doing any great amount of dentistry in these isolated stations. The commanding officer of this station has been very much interested in the work and has had me give blackboard lectures both to the men and officers.

I have written on the back of the pictures about each one.

Sincerely yours,

Edwin K. Busse


Categories: Brought to Light

Curing Cancer (No, Not Really) With HTML5 (Sort Of)

CKM Blog - Wed, 2014-11-05 09:49

Here’s a talk about federated search and Amalgamatic that I gave at HTML5DevConf in October. Hopefully, the conference will post a better quality video where you can actually see the demos. But for now, this is what I recorded.

Categories: CKM

Chunked Uploads with JQuery File Upload and Ruby on Rails

CKM Blog - Tue, 2014-10-21 08:13

I was inspired by this thread on the Google Hydra-Tech forum to put together a short tutorial on chunked uploads with jQuery file upload and Ruby on Rails.

There’s a nice example on GitHub for using this plugin with Rails, so we don’t need to do this from scratch. To see how this plugin works without chunked file uploads, clone the example


bundle, rake:db, rails server, and go to port 3000. You should see a nice UI for file uploads.

Try uploading a small file (under 500k). It works well, has a nice looking upload bar that flashes for just a few moments, and allows you to delete or cancel an upload. Now try uploading something a little bigger, maybe around 500MB. The progress bar will really come in handy here, but once it is complete, your server will most likely hang for a few minutes (at least). A file a few GB in size, while permitted, will take even longer and may slow down your web browser and localhost server to the point where it is unusable, and you need to go off to terminate a few processes manually through the command prompt.

At some point, you’ll probably start wanting to use the chunked file uploads feature, which splits the file into smaller pieces and submits them, one after the other, across the wire to your server.

To activate chunked file uploads, open the jquery-fileupload-rails-paperclip-example app and navigate to the views/uploads/index.html.erb file. At the bottom of this file (line 118 on my system), you’ll see a call to:


To use chunked file uploads, replace the above bit of code with:

$('#fileupload').fileupload({ maxChunkSize: 1000000 maxFileSize: 1000000 * 10000 });

Note – these values were chosen to illustrate the app working, you may want different values in production. For more on chunked file uploads, check the documentation.

Give it another try (you may need to reload the javascript for your change to take effect. Upload that medium size (at least a few dozen MB to see the full effect) and watch your dev server spin. You’ll notice that the controller for processing a file is getting called repeatedly for each chunk.

Watch your server log as rails processes the upload, and you’ll see that the controller is called repeatedly as you upload the file. The file uploader is splitting the medium sized file into 1 mb sized chunks and submitting them sequentially to the server.

Great, except.. refresh the page.

The rails app is processing each chunk as if it were a separate upload. Keep in mind, this has nothing to do with the jquery file uploader plugin, it’s doing exactly what we asked it to do – split up a file into small pieces and submit each one to the server. We just need to change how we’re processing this on the server side.

Before we go on, go ahead and delete those files (the fastest way is to check the box next to the upper menu delete button).

To process each chunk as part of a single file, rather than as a separate independent file upload, take a look at the create method in the uploads_controller.rb controller.

The first line

@upload = Upload.new(params[:upload])

creates a new upload object and processes it as a single file upload. You’ll need modify this to process it as a chunk rather than as a complete file.

There are plenty of ways to do this. To keep it all contained in an example, I’ll just go ahead and hack the controller. Remove the line above and replace it with the following code (entire method posted to avoid confusion about what to paste where)…

def create @temp_upload = Upload.new(params[:upload]) @upload = Upload.where(:upload_file_name => @temp_upload.upload_file_name).first if @upload.nil? @upload = Upload.create(params[:upload]) else if @upload.upload_file_size.nil? @upload.upload_file_size = @temp_upload.upload_file_size else @upload.upload_file_size += @temp_upload.upload_file_size end end p = params[:upload] name = p[:upload].original_filename directory = "uploads" path = File.join(directory, name.gsub(" ","_")) File.open(path, "ab") { |f| f.write(p[:upload].read) } respond_to do |format| if @upload.save format.html { render :json => [@upload.to_jq_upload].to_json, :content_type => 'text/html', :layout => false } format.json { render json: {files: [@upload.to_jq_upload]}, status: :created, location: @upload } else format.html { render action: "new" } format.json { render json: @upload.errors, status: :unprocessable_entity } end end end

Note – to keep things simple, I hard coded a new upload directory into the method, so you’ll need a top level “uploads” directory in your rails app for this to work.

In this method, we are now reading the upload parameters into a temporary upload object. We then look for an upload object with that file name (yes, different uploads could have the same file name, so you’d need a different approach for production). If that object doesn’t exist, create it, and treat the file chunk as if it were a new upload. If it does exist, retrieve it and append the newly uploaded chunk to the existing file. You do this over and over until the last chunk is processed (there’s also a running counter for file size).

Give it a try and refresh the screen. This time, you should see only one file upload, and you should be able to retrieve that file from your uploads directory. You may also notice that the long lag time between the status bar completion and the actual file upload completion is much shorter now, as the file is getting written to disk in small increments (you don’t have to convert the entire temp file upload on the server at once after upload, just the last chunk).

One note – some of the functionality of the upload plugin (such as delete) will no longer work with the new directory location.

So, should I do chunked file uploads?

The general approach above, with some modifications, does make it possible to process bigger files and stick with a pure ruby solution, and it could take care of the problem of medium file uploads that need to be chunked but perhaps don’t require an industrial strength solution.

However, if you want to allow really big file uploads, you might want to consider a solution that allows a user to upload a file to box, dropbox, google drive, etc, and then transfer it to your server from there as a background job. In fact, there’s a very nice gem from hydra labs called “browse everything”  that provides this functionality and integrates nicely with sufia. If you’re already using the “browse everything” type approach, you might just go ahead and limit direct non-chunked uploads to small sized files that won’t tax the system rather than managing the complexity overhead of a solution that sits in between.

In addition to the obvious problems I dismissed with a bit of hand waving and vague excuses about this being for to a sample exercise, there are other issues to consider with large file uploads. What do you do about partial uploads? Partially uploaded files where the user closed the connection or lost the network connection? Checksums (we can check the sum on each chunk, but were the chunks assembled properly on the server)?

Chunked file uploads are a very useful way to get that middle ground, and I suspect many of your users would really appreciate being able to upload medium size files without having to create an external account. I just want to emphasize that will the above approach can work, there’s a lot to consider here.

Categories: CKM

Introducing Amalgamatic

CKM Blog - Thu, 2014-10-16 07:40
“Search!” by Jeffrey Beall licensed CC BY-ND 2.0

Academic libraries offer many resources, but users cannot be expected to search in, say, a half dozen different interfaces to find what they’re looking for. So academic libraries typically offer federated search.

Sometimes, a solution is purchased. Many libraries, for example, use 360 Search.

Here at UCSF, we are among the libraries that have built our own federated search. Twice.

There are (at least) three ways to pull data out of other resources in real time.

  1. Cool, they have an API for that!
    This almost never happens.

  2. I will screen-scrape the #*%!?@ out of your website!
    This is by far the most common scenario.

  3. Web New-dot-Oh: It’s full of JavaScript that injects the content.
    An edge case, but one that is becoming more important all the time. Make friends with PhantomJS to scrape these sites.

When trying to implement these solutions, a common scenario is to build your screen-scraping federated search tool with traditional server-side languages like Java or PHP.

These strategies and technologies bring with them pitfalls to be avoided. Recompiling your WAR every time one of your target systems modifies their HTML layout, anyone?

Here’s another pitfall: Our group built a solution years ago (our first one) that is implemented in Drupal with no external facing API. So, if I want to experiment with a different results interface, I need to write it in Drupal. This tight coupling prevents experimentation with other technologies or things that don’t fit neatly into the Drupal paradigm.

A lot of the pitfalls can be avoided by following sound software architecture principles. But one thing should be uncontroversial:

No programming language has a more robust and widely-understood set of conventions and tools for processing blobs of HTML than JavaScript.

So how about building your federated search server using Node.js? Or maybe even take it a step further and just let your user’s browser execute the federated search entirely by itself, no need to talk to your server! If it’s all just JavaScript, why not?

That is our approach this second time around.

First, we wrote a pluggable, extensible federated search tool called Amalgamatic.

Second, we wrote the plugins that we needed to search the resources we were interested in:

In the course of writing these plugins, we used all three of the techniques described above (API, scraping HTML, and using a headless browser to get JavaScript-generated content).

Third, we used Amalgamatic to expose federated search on our API server. (source code)

Fourth, we set up a prototype search interface to use that API. (source code)

Lastly, because we could, we used Browserify to create a demo showing how to use Amalgamatic so that all the retrieval and processing happens in the browser—no need for an intermediary API or search server! (source code)

I hope others find this work useful. Use Amalgamatic, ask questions, file issues for bugs or feature requests, and write and publish your own plugins.

(Or tell me about your project that already does this better and I need to fold up shop or at least steal all your ideas.)

While I’m at it with the small-text thing, here’s a caveat on the Browserify-ed version: The one thing the browser couldn’t do was launch the PhantomJS headless browser for scraping sites that depend on JavaScript execution to display results. Fortunately for us, that was needed in the LibGuides plugin only. And LibGuides offers an API, so if we really wanted LibGuides results, we could use the API. We initially implemented it that way, actually, but found that the API results differed from the LibGuides search page results. We thought that might be confusing to users, so we went with PhantomJS-assisted scraping.

Categories: CKM
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