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JAMA Network Reader

Mobilized - 1 hour 37 min ago

Interested in reading JAMA articles on the go? You’ll be happy to know that because UCSF Library is a JAMA subscriber, our patrons have access to the latest year’s worth of content from all 10 JAMA journals on the JAMA Network Reader.

The Reader works across all devices — phone, tablet, and desktop — to give you free, instant access to the research, reviews, and viewpoints in all JAMA Network journals, including those published online first and with embedded video. It’s browser based and available as a Chrome app or Safari extension to allow for offline article viewing (articles are only available for online viewing on Mozilla and Internet Explorer through the Reader website). The option to read either online or off saves storage space on your device and gives you the ability to easily access the article later.

Additionally, there are no manual updates needed, and Online First articles and new issues appear automatically.

To take advantage of this benefit to UCSF’s JAMA subscription, you will need to access the JAMA Network Reader while on the UCSF network or click through to the JAMA Network from the library catalog if you’re off campus. Look for the link to the Reader on the top of the right sidebar of every article page. For more detailed instructions, please visit the JAMA Network Reader website and see the section “How to access through your institution.”

Also visit the Reader site to learn more about installation and offline reading.

Image from JAMA.

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Categories: Mobilized

1920’s Medical Crossword Puzzle Answers

Brought to Light Blog - Thu, 2014-09-11 08:56

No spoilers here. Click through to see the answers.

If you haven’t seen the crossword puzzles, yet, check out the previous post on the Children’s Hospital of San Francisco Alumnae Association collection.

Answers to crossword puzzle by Adelaide Brown, M.D. Children’s Hospital of San Francisco Training School for Nurses Little Jim yearbook, 1925, page 53, MSS 2006-17.

Answers to crossword puzzle. Children’s Hospital of San Francisco Training School for Nurses Little Jim yearbook, 1925, page 50, MSS 2006-17.

 

Categories: Brought to Light

Automatic backups with Box Sync

Mobilized - Wed, 2014-09-10 08:40

Given San Francisco’s history of earthquakes, I should be better prepared.
My earthquake kit has a flashlight, portable radio, first-aid kit, and enough dehydrated food rations to last a few weeks. I’m probably better prepared than most, but I’m still lacking an adequate supply of water, spare clothes, cash, street maps, and emergency contacts. In terms of earthquake preparedness, I’m woefully short of ready. Emergency preparedness is a great analogue for data disaster recovery. Investing some time in being prepared could potentially pay huge dividends later on; preparing yourself for the worst is often easier than dealing with disasters as they unfold.

If you’ve owned a computer in the past decade, chances are you have either experienced a hard drive failure or know someone who has. Data from Backblaze –– an online backup provider –– outlines how failures can occur due to manufacturing defects, as well as wear-out failures. Wear-out failures unsurprisingly increase with disk age. Unlike traditional spinning hard disks, the increasingly popular solid state drives do not have moving components and thus are less likely to fail mechanically. Solid state drives, however, are not immune from wear-out. Regardless of the kind of drive you own, having a secure, automatic, online backup is a great practice.

UCSF Box

If you’re staff, faculty, or a student here at UCSF with MyAccess privileges, you already have access to UCSF Box. Box is one in a crowd of cloud-based storage providers, competing with Dropbox, Mozy, Skydrive, SugarSync, Amazon Cloud Drive, and many others. UCSF Box provides 60 gigabytes of personal storage with a file size limit of 5 gigabytes. You can use Box to store, access, and share data.

Cloud vs Network Shared Drive

Box, like many other cloud services, offers some advantages over traditional storage on a network drive. (Note that a network drive is not the hard drive on your computer — it’s backed up storage space provided on your school or workplace server. Typically, you must be on-site to use it.)

  1. Access from anywhere. Once your data is up in your Box account, you can access it from anywhere with an internet connection. That includes directly via their website, through mobile applications on both Android, Phone/iPad, and Windows Phone.
  2. Share files easily. In Box, you can share files and folders quickly with anyone. You can generate a hyperlink to share your data, then customize the access settings according to your needs. Find out more about sharing files with Box.
  3. Add tasks, discussions, and comments to files.

There are a few drawbacks with using Box at UCSF, most notably that it cannot be used for FERPA or ePHI information. Also, if you have data exceeding 5gb per file, or 60gb in total, traditional network storage would be more suitable. Otherwise, the benefits of portability between devices and the enhanced suite of features make Box a great option.

Box Sync

Box Sync is a great feature, similar to other cloud storage offerings, that integrates a folder on your Mac or PC with your Box.com account. Anything added or modified within this folder is automatically backed up. You can modify the contents of the folder while you are offline and the changes will be applied the next time you connect to the internet.

To setup Box Sync, follow the instructions below.

  1. If you haven’t setup your Box account yet, do so by visiting UCSF Box (or Box.com if you are not part of the UCSF community)
  2. Download the Box Sync client from here
  3. Follow the install instructions for your operating system here
  4. When you first launch Box Sync, you can choose a custom location for your Box Sync Folder.

In my case, I’ve setup my Box Sync folder in my User Directory (the default location). I’ve added a folder entitled “PowerPoint Presentations” as well as a sample document entitled “Sample Word Document.” The Box Sync application has syncing turned on.

When I login to my Box account, I see that both the folder and the document have been uploaded. Anything I place in the Box Sync folder will be uploaded, including documents seeded within other folders.

Go On, Be Prepared

Don’t wait to take advantage of your space on UCSF Box. It could save you enormous hassle and heartache if (when!) your local hard drive fails. If you don’t have UCSF privileges, you can still use a Box.com free account or a competing solution, though your amount of space and/or cost may vary. If you take a few minutes to set up some kind of cloud-based file storage, you won’t be sorry.

 

No related posts.

Categories: Mobilized

Using EndNote for Collaboration: EndNote Basic (aka EndNote Web)

In Plain Sight - Mon, 2014-09-08 12:04

A previous post outlined a simple way to share references using EndNote’s “traveling library” features. However, EndNote Basic (previously known as EndNote Web) offers more sophisticate features for sharing references with colleagues.

Just to remind you, there are now two versions of EndNote, desktop EndNote and Endnote Basic.  The latter is a separate application from the desktop version. It’s free, and was formerly known as Endnote Web. EndNote Basic is essentially a web-based stripped down version providing users with the ability to store 50,000 references, 2GB of file storage, 21 bibliographic styles, 5 online search connectors, and 9 import filters.

With EndNote Basic it is possible to create groups which you can share with others.  Groups can be created on the basis of either read or read/write.

  1. Select the Organize tab from the top of the screen, and then click on Manage My Groups:
  2. You’ll notice there is a column with options for sharing. Check the box next to Share and then click the Manage Sharing button:
  3. Groups can be shared with anyone that has an EndNote Basic account.  You can allow people to view your citations, or you can allow them full access to the group using the Read & Write option.  Be aware that if you allow someone Read & Write access, they can add, delete, and modify the citations in that group. You can modify or turn off sharing at any time. 
  4. When the other person logs in they’ll see the shared groups:

 

 

 

 

 

 

View this short online tutorial to learn more.

Note however that whilst references can be shared within a group, PDF attachments cannot be shared due to licensing restrictions.

 

Categories: In Plain Sight

Random Forests and Datashare at the CDL Code Jam

CKM Blog - Fri, 2014-09-05 11:28

The California Digital Library hosted a code jam earlier this month at the Oakland City Conference center.

This gathering brought together librarians and developers from University of California campuses for a series of working meetings with an eye toward system-wide projects, especially involving data curation.

In the spirit of an informal, code-jam style meeting, I presented a bit on my recent experiments using machine learning to categorize data. As a starting example, I applied a random forest to suggest subject keywords for data sets uploaded to the recently launched DataShare website.

A researcher who uploads a data set to Datashare through the datashare-ingest app is prompted to provide keyword information along with other metadata describing the data set. One relatively common keyword is “middle-aged”.

http://datashare.ucsf.edu/xtf/search?f1-keyword=Middle%20Aged

For the code jam, I showed one possible way to use these existing records to train a random forest to determine whether a new dataset should be tagged with the keyword “middle-aged”.

For this particular exercise, there isn’t a great deal of data – we’d need a much larger data set to really apply this. However, the small dataset has some advantages for exploring the use of random forests, as it’s possible to visually inspect the input and gain a better understanding of how the random forest categorization is working.

“Middle aged” is a relatively good term to use for an experiment, as it isn’t as obvious (or as objective) more technical terminology. Highly technical keywords often show up repeatedly in the data set, and are often very predictable. More subjective and less technical keywords such as “middle aged” may apply to a wide range subjects, and they may show up in some records but not in others, as some researchers include the keyword and others don’t. Random Forest classification can be particularly useful in this case, as these subjective keywords are more likely to be applied when they don’t show up in the description, title, or technical methods for a particular dataset.

For example, here’s a record tagged with the keyword “middle aged”.

To get started, I approached this with a simple “bag of words” approach, with a small modification. Rather than taking a very large bag of words for all records (or a sample of all records) in Datashare, I limited the count to words that show up in records with the keyword “middle aged”.

data: 14
changes: 12
disease: 12
alzheimer: 11
diffusion: 10
dti: 9
subjects: 9
images: 9
slice: 9
brain: 8
ftd: 8
imaging: 8
axial: 7
white: 7
matter: 7
tracts: 7
reductions: 7
acquired: 7
gwi: 7
center: 7
diffusivity: 7
thickness: 6
type: 6
symptoms: 6

(for the full list, run the wordcount_summary.py script in the github repo).

I used this bag of words to populate a random forest. For each record, I created a vector indicating the word count for each of the most common words in each dataset, using the title, abstract, and methods as text fields.

Here’s the bag of words for a single record that includes the “middle-aged” subject tag:

ark+=b7272=q67p8w9z
data 1
changes 7
disease 0
alzheimer 0
diffusion 6
dti 5
subjects 2
images 4
slice 0
brain 2
ftd 0

And here’s the bag of words for a single record that doesn’t contain this keyword:

data 5
changes 6
disease 4
alzheimer 4
diffusion 0
dti 0
subjects 16
images 1
slice 0
brain 10
ftd 0

Each of these records is converted into a vector containing the word count along with information about whether it was tagged with the keyword “middle-aged” (for the python scikit-learn library, I expressed this as a binary 0 or 1).

A categorization problem like this, where a bag of words is used as the basis for determining whether a record belongs in a particular category, can be approached with a number of different supervised learning techniques. Logistic Regression and Decision Trees are common approaches, and Random Forest is a particularly accessible and often effective algorithm for many categorization problems. I used a Random Forest classifier here, though other algorithms might turn out to be more effective.

For this application, I converted each record into a vector representing the bag of words, with each position representing a common term, and each value representing the number of instances of that word. I ignore a number of stop words and common terms, but there’s a lot more that could be done here, especially around identifying common phrases rather than single words. Each vector, along with an indicator representing whether this record was tagged with the subject “middle aged”, is then used to train a random forest classifier.

The rforestDS-Middle-Age.py script contains python code using scikit-learn to train and evaluate a random forest classifier on the Datashare records for the “middle aged” keyword tag, using the strategy described above.

Note that if you run this multiple times, you’ll get slightly different output. This is probably amplified by the relatively small number of training samples.

The train data score indicates how well the random forest categorizes the records that were used to train it. Because of the small sample size and relatively specific vocabulary, the assessment is fairly high.

Train data score: 0.941176470588

While it is interesting to observe the Random Forest’s assessment of how it performs on its own training set, a common practice is to split the training data into a training set and testing set (often at a two-thirds training, one-third testing ratio). You can then use the testing data (which was not used to build or train the random forest) to evaluate the accuracy of the classifier. I didn’t in this particular case, as the training set was very small and this is a small experiment/exercise, but it would be an important step on a larger dataset where we plan to make real use of a classifier.

Random Forests can also estimate the relative importance of the classifiers (in this case, the importance of the word count for each of the most common words in determining whether a record has been tagged with the subject “middle aged”). Here’s the feature importance estimate for a run of the random forest. The numbers will change slightly each time the forest is run.

data: 0.115221184049
changes: 0.0497659524022
disease: 0.0414350226064
alzheimer: 0.0438029075727
diffusion: 0.0870807358224
dti: 0.0287297792369
subjects: 0.0548861615427
images: 0.0783953700445
slice: 0.401884434536
brain: 0.0378775508884
ftd: 0.0609209012994

Although such a small sample size isn’t ideal for building a useful classifier, it can be illuminating, as the data set is small enough to hint at why certain words are so important. “Slice”, for instance, probably wouldn’t be such a strong predictor for whether a record should be tagged as “middle aged” in a larger data set. This is almost certainly a quirk related to our small sample size.

The output for this script is stored in the “categories” folder in a file named “1-Middle-Aged.txt”.

ark+=b7272=q6154f00,””
ark+=b7272=q61z429d,””
ark+=b7272=q62z13fs,”Middle-Aged”
ark+=b7272=q65q4t1r,””
ark+=b7272=q66q1v54,”Middle-Aged”
ark+=b7272=q67p8w9z,”Middle-Aged”
ark+=b7272=q6bg2kwf,””
ark+=b7272=q6cc0xmh,”Middle-Aged”
ark+=b7272=q6h41pb7,””
ark+=b7272=q6kw5cxv,”Middle-Aged”
ark+=b7272=q6mw2f2n,””
ark+=b7272=q6pn93h6,””
ark+=b7272=q6qn64nk,”Middle-Aged”
ark+=b7272=q6rn35sz,””
ark+=b7272=q6td9v7j,””
ark+=b7272=q6x63jt1,””

To apply the random forest to all subject tags, run the rforestDS.py script. You should see similar output for each keyword tag, along the training data score and feature importance estimates. To assemble all the estimates into a single file, run the MergeFiles.py script.

GitHub repository for this exercise

Github repository for Dash (formerly Datashare)

Categories: CKM

Recent Accession: Children’s Hospital, San Francisco Nursing School

Brought to Light Blog - Thu, 2014-09-04 11:22

We’ve recently acquired a collection from the Children’s Hospital of San Francisco Nurses’ Alumnae Association, MSS 2006-17. Let’s break that down.

Children’s Hospital of San Francisco Training School for Nurses Little Jim yearbook, 1925, page 45, MSS 2006-17.

The California Pacific Medical Center’s historical timeline and UCSF History site prove quite useful for untangling this history. In 1875 the Pacific Dispensary for Women and Children was founded in San Francisco. It underwent a name change and became, more recognizably, the Women’s and Children’s Hospital. Under the leadership of the pioneering Dr. Charlotte Blake Brown (1846-1904) in 1882, the hospital began offering a two-year training program for nurses– the first official of its kind on the West Coast. And in 1887, it finds a new home at the intersection of California & Maple streets. At this point, “the two-story hospital has 25 private rooms, open wards, a cow barn, chicken yard, and laundry. Total cost, with furniture and equipment: $26,000.” The University of California Medical School (that’s us– UCSF!) begins partnering with Children’s Hospital in 1915 to teach medical students.

Group of nursing students, circa 1925, MSS 2006-17.

Which brings us just to about the time period of this collection. Donated by the granddaughter of Ruth Steuben, an alumna of the Children’s Hospital Training School for Nurses, the material covers the education of Steuben, roughly 1925-1929, and includes class notes, yearbooks, photographs, and a uniform apron. Digital copies of Steuben’s school records as well as photographs and letters from the mothers of children nursed by Steuben soon after her graduation are also included. Below, a photograph of Ruth with her graduating class, December 1927, from the Little Jim yearbook.

Class of December 1927, including Ruth Steuben. Children’s Hospital of San Francisco Training School for Nurses Little Jim yearbook, 1926, page 22, MSS 2006-17.

And a photograph of many of the same students at a nursing school reunion event in May 1948.

Reunion of nursing school graduates, May 1948, MSS 2006-17.

And now, for your further enjoyment: crossword puzzles! The 1948 Little Jim yearbook includes not one, but two crossword puzzles. The first was created by Adelaide Brown, M.D. (1868-1933) who was the daughter of Dr. Charlotte Blake Brown– both were longtime activists for women and children’s health.

Crossword puzzle by Adelaide Brown, M.D. Children’s Hospital of San Francisco Training School for Nurses Little Jim yearbook, 1925, page 48, MSS 2006-17.

Crossword puzzle. Children’s Hospital of San Francisco Training School for Nurses Little Jim yearbook, 1925, page 50, MSS 2006-17.

Please see our other collections regarding the Children’s Hospital of San Francisco Nursing School Alumnae Association, MSS 89-20 and MSS 91-101. Read more about Dr. Charlotte Blake Brown in this fascinating article, The San Francisco Experiment: Female Medical Practitioners Caring for Women and Children, 1875-1932, by Meredith Eliassen and published online in Gender Forum.

Categories: Brought to Light

Fall 2014 Tech Clinics Announced

Convergence - Thu, 2014-09-04 09:38

Have you been working on CLE or multimedia projects this summer in preparation for fall courses? If you have, I am sure you have questions or even better, want to share some of the great work that you have done. Just in time for the Fall 2014 semester, we are excited to announce dates for the upcoming Tech Clinics offered through the Learning Technologies Group and UCSF Library. You can register for a Clinic today at tiny.ucsf.edu/LTGClinics.

The Learning Technologies Group will offer one Multimedia Clinic and one CLE Clinic a month throughout the rest of the year. The Clinics are offered at no cost to all UCSF community members. Here are some recent changes to the CLE that you may be interested in learning more about at an upcoming CLE Clinic:

  • The recent CLE Refresh
  • Web conferencing alternatives
  • Tips for managing CLE courses from semester to semester
  • Improvements to the Quiz activity
  • Recommendations for designing courses for students using mobile devices

New additions to Tech Clinics offerings include:

  • Attend a Clinic remotely using WebEx
  • Attend a CLE Roundtable to collaborate with other staff and faculty using the CLE
  • Film a faculty interview in the eLearning Studio during a Multimedia Clinic
  • Discover use cases for using iPads and mobile devices in the classroom at a Multimedia Clinic
  • Learn a new application using Lynda.com in the Tech Commons at a Multimedia Clinic
  • And of course, train new staff!

Each Clinic offers short presentation/demos on popular topics throughout the day as well as one-on-one support opportunities with Learning Technologies staff.

CLE Clinics Fall Schedule (click below for more information and to register)

Multimedia Clinics Fall Schedule (click below for more information and to register)

*Have the Learning Technologies Group helped you recently? During the Multimedia Clinic on Friday, September 12, we will be filming testimonials on working with the UCSF Library and Learning Technologies Group. If you are interested in participating and filming a 30-60 second testimonial during the September 12 Clinic, please register using the link above or contact the Learning Technologies Group.

We hope to see you there!

Image Credit: “Light-Bulb” designed by Phil Goodwin from the Noun Project
Image Credit: “Refresh” designed by Chris Dobbins from the Noun Project
Image Credit: “Check-Mark” designed by DEADTYPE from the Noun Project

 

 

 

 

Categories: Convergence

Using EndNote for Collaboration: the Traveling Library

In Plain Sight - Wed, 2014-09-03 13:23

A Traveling Library refers to the formatted citations in your Word document and is created for each Word document when formatted using EndNote and Cite-While-You-Write (CWYW):  it’s a subset of your EndNote library which contains only the citations that appear in your paper. Each time you format a citation (e.g. insert a reference) EndNote will look in your open library to find the corresponding reference. If the library is not available or not open, EndNote uses the “traveling library” for reference information. This allows you to collaborate with other authors on a paper without each author having the same EndNote library because reference data is kept with each formatted citation. The reference data saved with each citation includes all fields except Notes, Abstract, and Figure.

When someone e-mails you a MS Word document that has been created with EndNote citations you can export the “traveling library” from Word into a new or existing EndNote library on your own computer by following these steps:

  • Have the Word document open and go to the EndNote tab (in Word 2007 +).
  • In the most right column, click on “Export to EndNote.”


 

 

 

  • Choose “Export Traveling Library”. Follow the directions. You’ll be guided to add those references into either an existing EndNote library (by selecting a library from the drop-down list or using Browse to locate the library) or a new EndNote library.

 

 

 

 

 

 

Please note that this will only work if the Word document citations were created using EndNote, and the EndNote coding still remains in the document (i.e. it wasn’t converted to a plain text document before you received it).

Categories: In Plain Sight

Personalizing CLE Courses for Students

Convergence - Thu, 2014-08-28 13:41

Starting a new online course can sometimes be a daunting task. A student may look at a course page and see a never-ending list of activities and resources for them to view or complete. If a student opens up a course like the one pictured below, they might become paralyzed by the dreaded scroll of death. They might wonder where do I even begin? And over time, they may wonder Which resources or activities have I already viewed or completed? How do I know if I’m even getting anywhere? Luckily, Moodle, the learning management system that powers UCSF’s CLE, provides ways for us to help students go through their online courses in a personalized fashion. This may mean selectively introducing content, branching activities based on performance, or merely keeping activities hidden until they are needed by the learner. Moodle’s conditional activity features provide a helpful way for students to see their progress in a course. This is especially useful for asynchronous learning, because it allows the learner to be in control of their progress over time versus waiting for the next content to be made available by the instructor. Some common uses of Conditional Activities might be:

  • Don’t show course content until learner accepts an agreement
  • Don’t show course content until learner takes a pre-test
  • Show post-test after learner views last module
  • Provide certificate of completion when learner earns certain score on post-test
  • Show remedial or advanced course content or Topics based on a Quiz or Assignment grade

Employing conditional activities in a CLE course can get complicated pretty quickly. It’s best to start simple and stay simple. So, let’s start simple! Using conditional activities has two parts: 1) Activity Completion and 2) Access restrictions. Our faithful readers may remember that we posted about Activity Completion back in November, but let’s take a deeper dive now.

Activity Completion

When employing the conditional activity features, you’ll want to set up Activity completion first, then move on to adding access restrictions. Activity completion is enabled in the Course Settings for a course. It’s best practice to enable this for a course before you start adding Activities and Resources, so the setting is automatically enabled. If you are enabling Activity completion after you’ve added items to the course, you will have to go back and enable each Activity or Resource individually.

For each course Activity or Resource, you can set the completion settings as you choose. There are three main options for each course activity or resource:

  • Do not indicate activity completion
  • Students can manually mark the activity as completed
  • Show activity as complete when conditions are met

For the option where certain conditions must be met, you can indicate the conditions you wish. The simplest is “view”. This means the student merely needs to open up the File or URL once and then, it is deemed complete. Graded items, like the Quiz, Assignment, or a SCORM package (like an Articulate presentation), can require a certain grade to be deemed complete. The Forum has the most complex activity completion criteria with options to require a certain number of posts or replies. When the conditions are met, check marks appear in the boxes for each activity.

Access Restrictions

The second part to employing Conditional Activities is using the Access restrictions. This setting enables Instructors to restrict the availability of any activity, resource, or even a course Topic according to certain conditions such as dates, viewing the activity, a certain grade obtained, or activity completion is fulfilled. The use of access restrictions personalizes the course experience for the learner. The appearance of activities depends on each student’s own completion of prior activities. When these access restrictions are set, each student’s course might look slightly different, because each student may be further along than other students are. In the Restrict access options, an Instructor can indicate a date that you expect the completion criteria to be completed by, however this date is not shown to students. It is only displayed in the Activity completion report that is available to Instructors, such as the one below. A quick, but important note about Activity completion: UCSF’s CLE server gets triggered every 10 minutes to refresh activity completions. This means that although a student may have completed the activity, the criteria won’t necessarily register for another 10 minutes. I hope this blog post has whet your appetite for exploring the course personalization options available to you with the CLE. As you can probably tell, the Restrict access options can get a lot more complicated and we’ll go into that in a later blog post. Until then, please feel free to contact the UCSF Learning Technologies Group for any of your online learning needs! Laptop Image Credit: Kristen McPeak from the Noun Project

Categories: Convergence

Through the Years: The History of Dr. Eddie Leong Way

Brought to Light Blog - Thu, 2014-08-21 09:23

In the spirit of UCSF’s 150th anniversary, a new addition to the archives has been made: the history of our very own Dr. Eddie Leong Way.   The addition is very much relevant to the anniversary, as Dr. Way himself has contributed much to the school’s 150 years.  In fact, he makes up many of those years, himself.

E. Leong Way and Chauncey D. Leake in Atlantic City at the first Federation of American Societies for Experimental Biology (FASEB) meeting after WWII, April 1946.

Born in San Francisco, Dr. Way earned his bachelor’s degree from UC Berkeley before going on to obtain his PhD in pharmaceutical chemistry from UCSF’s very own School of Pharmacy.  However, his involvement with the school did not simply stop at his educational background.  Dr. Way worked as a professor at UCSF for years after his graduation, only retiring in 1987.  His career primarily focused on the development of physical dependence and tolerance of opiates.  It comes as no surprise, then, that such extensive work has contributed to creating a generally much more improved and deeper understanding of addiction.

Spending some days in the archives, I had the fascinating task of working through Dr. Way’s time and work here at UCSF, from the beginning of his career to years after its official end.  As I leafed through pages and pictures, both brittle with age and sleek with freshness, I felt the pleasant weight of history at my fingertips.   Some of the files dated back to as early as 1939, and some as recent as 2008.

E. Leong Way and Harry Iwamoto, UCSF School of Pharmacy Class of 1938, March 10, 1986.

All sorts of documents made their way to the archives.  Several of his publications and publication listings; various correspondences with other faculty members and students; notes and slides from his own lectures; even invitations and party photos!  Work and play all mingle together in the collection to form the personal history of this astounding individual.  His files dictating his time and effort spent towards the betterment of the UCSF School of Pharmacy and even the world of pharmacy as a whole are now preserved in UCSF’s extensive and detailed archives, where they shall most certainly remain safe and sound.

For more information please see the library catalog record and finding aid for the Way papers.

Alex Giacomini was born and raised in the San Francisco Bay Area. She is vastly interested in writing and the humanities, and is currently a communications intern in UCSF’s School of Pharmacy.   Alex is a rising senior at UC Berkeley, where she is working to attain her Bachelor of Arts in English Literature.

Categories: Brought to Light

Redesign Your Website in 4,000 Easy Steps

CKM Blog - Tue, 2014-08-12 16:33

Earlier this month, Rich Trott and I delivered a session at the University of California Computing Services Conference (UCCSC) in San Francisco. It was about our experience using an approach of continuous iterative improvements and frequent feedback to help keep our site fresh and meeting user needs. We talked about why this approach has been working better than the tradition complete redesign that might happen every few years (or not.)

If you can’t wait to hear more, see the slides with notes.

Or if you’re more of the video type, you can check that out too.

Let us know about your experiences using this kind of approach to website upkeep and positive user experience. What works for your site or organization?

Photo by chexee

Categories: CKM

The Life and Times of a Newbie Intern

Brought to Light Blog - Tue, 2014-08-12 10:35

Before me there stood a great, big wall.  An obstacle.  A fortress.  Well, metaphorically speaking, in any case.  However, the five archival boxes full of various documents and files seemed as large as the tallest gate to me.  Being a lowly intern, I must admit that I was a bit intimidated.  After all, it was my responsibility to sort and organize all of these files.

The documents all pertained to the life and career of Dr. E (‘Eddie’) Leong Way, one of UCSF’s oldest alumni, and a great contributor to the understanding of opiate addiction and reliance.  Unfortunately, their previous keepers did not properly store the files.  They were in some small state of disarray, stuffed in varying folders and envelopes, stacked on top of each other, and even, in some cases, in incorrect boxes.

It was my job to remove the files from their initial place and sort them properly.  I took them out of their different folders and placed them in official, archival ones, meant for preserving and protecting files more efficiently than other folders.  Each folder must be labeled and numbered properly as well.  After that, they are to be placed in official, archival boxes.  And, lastly, I had to write up the inventories for each of the boxes.

It was a long, time-consuming task, requiring precision and a good deal of attention.  Admittedly, it was a bit frustrating at times.  However, that did not prevent it from being a great experience.  It was fascinating to get insight into the work required in the archives.  More importantly, it helped me understand the hard work others put into these tasks and others, as well as appreciate the importance of preserving and organizing the archives affectively and efficiently.  If I were to be perfectly honest, I wouldn’t trade the experience for anything.

For more information please see the library catalog record and finding aid for the Way papers.

Alex Giacomini was born and raised in the San Francisco Bay Area. She is vastly interested in writing and the humanities, and is currently a communications intern in UCSF’s School of Pharmacy.   Alex is a rising senior at UC Berkeley, where she is working to attain her Bachelor of Arts in English Literature.

Categories: Brought to Light

When Will EndNote X8 be Released?

In Plain Sight - Mon, 2014-08-11 12:31

Some of us dread the arrival of summer because that’s when the EndNote folks usually announce the release of a new version of the software and we have to start thinking about whether or not it’s worth upgrading (and if you have it installed on multiple workstations  in a teaching lab, where are you going to get the money?). As September approaches I was wondering what was the delay with X8. According to a post I found on Facebook there will be no new update this year.  You can read EndNote’s explanation here:

 

 

 

 

 

 

My thanks to Pedro from Brazil!

If you’ve working with version X7 you might want to upgrade to X7.1, for free. There are some enhancements to syncing between the desktop and online versions, so you might want to check this out. Details here. Download here.

 

 

Categories: In Plain Sight

Eric L. Berne exhibit marks the conclusion of the first phase of Eric Berne Papers Processing Project

Brought to Light Blog - Fri, 2014-08-08 13:10

The UCSF Archives & Special Collections would like to announce the opening of the new exhibit, “Eric L. Berne Archive: The Birth of Transactional Analysis.” This exhibit marks the conclusion of the first phase of the Eric Berne Archive Processing project.
Eric L. Berne (1910-1970) was a practicing psychiatrist, lecturer and author. Best known for his development of the theory of Transactional Analysis, Berne published dozens of scholarly articles in the field of psychoanalysis and was the author of eight major books, including the bestseller Games People Play.

Advertisements for Games People Play, the New York Times Book Review, August 14, 1966. Eric L. Berne papers, MSS 2005-08, box 4, folder 21 UCSF Archives & Special Collections.

The materials in the Archive were created by Dr. Berne (1910-1970) and by the organizations he founded: the San Francisco Social Psychiatry Seminars (SFSPS) and the International Transactional Analysis Association (ITAA). The Archive holds Berne’s personal and professional papers, including correspondence, writings, notes, conference programs, administrative records, photographs, and audio-visual recordings.

In the past nine months (September 2013-May 2014) project archivist, Kate Tasker has been working diligently to process six existing collections and two recently added accessions. As a result of this effort six detailed finding aids for the Eric Bern Archive consisting of 77 boxes or 41.8 linear feet were added to the Online Archive of California. Kate also organized and compiled an inventory for the Eric L. Berne Rare Book collection that includes over 300 books from Berne’s personal library and copies of his published works. With the help of our cataloger, Bea Mallek, these volumes were added to the UCSF Library catalog and can be consulted in the Archives & Special Collections reading room.

Costume party, August 1959.Eric L. Berne papers, MSS 82-0, box 2, folder 10 UCSF Archives & Special Collections.

Another important achievement was the digitization of more than 400 unique documents, containing Eric Berne correspondence (including letters from significant figures such as Alfred C. Kinsey, Paul Federn, and Karl Menninger), writings, educational records, lecture drafts, announcements and publications from the SFSPS and the ITAA as well as photographs. The Eric L. Berne digital collection, an educational portal containing information about Eric Berne, his studies and writings is now accessible to researchers and general public worldwide.

Announcement card for the opening of Berne’s San Francisco office, undated. Eric L. Berne papers, MSS 2003-12, box 3, folder 4, UCSF Archives & Special Collections.

The exhibit highlights selected artifacts, photos and documents from the Eric L. Berne Archive at UCSF.
The visitors will be able to view Berne’s correspondence concerning the design and promotion of the board game “Games People Play” and a fully intact game set, edited typescript of his first book The Mind in Action, his glasses, an announcement about the opening of his practice in San Francisco, a selection of English and foreign language
editions of his book Games People Play and numerous photographs.

Photograph of the components of the Games People Play board game, based on Eric Berne’s best-selling book of the same title. Eric L. Berne Papers, 1929-1970, MSS 2005-08, box 4, folder 20, UCSF Archives & Special Collections.

The Eric L. Berne Archive is housed in the UCSF Archives and Special Collections. Detailed processing and digitization for these materials were made possible by generous support from 23 TA Associations worldwide and many individual donors through the ITAA. The UCSF Archives will continue working with the ITAA and its supporters to secure funding for the digitization of additional items.
Please view the online companion for this exhibit on the UCSF library website.
The exhibit will be on view on the 5th floor of the Parnassus Campus Library, beginning August 8th, 2014.

Categories: Brought to Light

Lynda.com is here!

Convergence - Thu, 2014-08-07 12:24

The web’s leading resource for online video tutorials is now available in CL240 of the Tech Commons! Lynda.com offers thousands of professionally produced video tutorials on a wide variety of subjects. This includes many of the tools that the Help Desk and Learning Technologies Group support, like Moodle, Articulate, Camtasia, and iMovie.

You can also sharpen your presentation skills, learn to properly light a video interview, or improve your screencasting techniques. Here are a few of our staff picks!

Screencasting Fundamentals  |  iMovie 10 Essential Training  |  Moodle 2.6 Essential Training  |  Foundations of Video: Interviews  |  Up and Running with Articulate ’13


If you are interested in using this service, follow the guidelines below:

  1. Reserve a block of time for “CL240 #3 (Mac)” here: tiny.ucsf.edu/reservemm
    Note: Lynda.com users take precedence on this workstation.
  2. Log in to the workstation and then double-click on the Lynda.com icon on the desktop. A browser will open and load the Lynda.com website, giving you access to the full Lynda.com catalog.
  3. When you are done, it is very important that you log out of the Lynda.com website before logging off the workstation. Click the “Log out” link in the top-right corner of the browser window. If you fail to do so, the account will be locked for other users.

In the future, we would like to expand this service to more than one workstation, so show your support by visiting us in CL240, watching some tutorials, and helping us spread the word to your colleagues!

If you have any questions, please send an email to LearningTech@ucsf.edu, or stop by the Help Desk in CL240 and chat with us.

Please note, the workstations in CL240 provide students, faculty and staff with the resources to create dynamic, multimedia content in supplement of the teaching and learning process at UCSF. Use of these workstations and Lynda.com for personal projects is strongly discouraged during normal business hours, and should never interfere with users working on UCSF sanctioned projects.

 

Categories: Convergence

Announcing Symfony Ember.js Edition

CKM Blog - Tue, 2014-08-05 13:30

We’ve spent a lot of time getting the configuration right for setting up Ember.js and EmberData to work with a Symfony backend. So we have decided to release a working example of getting this right:

Symfony Ember.js Edition

Background

The Ilios project is investigating a migration to Ember.js. Because we have a lot of PHP experience and a lot of PHP code, it makes sense to serve the content using Symfony. We chose Ember.js because of its convention over configuration approach and wanted to make as few customizations as possible.

EmberData provides a clean way to represent your data models in JavaScript and bind them to templates and controllers. It also has built-in REST functionality for keeping those models up to date on the server.

Specific Fixes Compiling Handlebars templates

Ember expects compiled Handlebars templates to be in the JavaScript Ember.TEMPLATES object instead of Handlebars.template. That’s fine if you put all of your templates in index.html like they do in most examples. In that case, Ember does the compilation itself.

However we wanted separate templates and routers in different files. This required pre-compiling the templates for Ember. Thankfully there is a Node.js application for doing this already called ember-precompile.

It is even supported in the latest version of Assetic. However AsseticBundle hasn’t been updated in a while, so we had to mess with the Composer definition to get this working. The Assetic compiler will fail silently if you don’t have ember-precompile installed in /usr/bin/ember-precompile. Hopefully a fix for that will be available soon.

Testing the API

We want test coverage for our API, but actually getting the right input proved to be a bit complicated. There is a demo controller test and a base test in the AcmeApiBundle in this distribution. You can use it as a starting point to make writing other tests easier.

JS Dependencies

We use Bower to install all of our dependencies, include them in the layout, and manage their version without checking the code into our repo.

None of this would have been possible without:

Categories: CKM

CLE Refresh Coming Tomorrow

Convergence - Fri, 2014-08-01 16:25

Tomorrow, August 2, the Collaborative Learning Environment (CLE) will undergo an update as detailed in last month’s blog post, Announcing the CLE Refresh! The CLE will be unavailable on Saturday, August 2, from 6 AM – 2 PM (PDT) to complete the upgrade to Moodle 2.6 (the original upgrade date was scheduled for July 26).

Here are just a few improvements to look forward to with the refresh:

A New Look and Feel: You will immediately notice the new CLE theme when logging in August 2 after 2pm. Take a look around and notice the new CLE Home Page – with quick access to your CLE courses and support resources.

Mobile Friendly: The CLE is now mobile friendly! Try visiting your summer or fall courses using your mobile device. The CLE will now scale to fit the device of your choosing!

10 Notable Features as Explained by Sean Gabriel McClelland: Last month’s blog post included Sean Gabriel McClelland’s Top 10 New Features: Summer 2014. Check it out and contact LTG or post a comment below if you have any of your own additions for this list!

Here are a few items that may cause some initial confusion, as well as explanations of the changes:

  • Course names now automatically display on top of page: You will notice that the name of the course now appears on the top of CLE course page. This is a great way to provide a consistent experience for students throughout CLE courses.
  • All content and enrollment is transferred and no content migration required: Unlike the CLE update last summer, you will not need to migrate any course content. All content and student enrollment will be in your CLE course on Saturday, August 2.
  • No more Collaborate web conference activity: Collaborate will no longer be available at UCSF or via the CLE. Read more in the blog post, Collaborate Retiring on August 2.

Of course we will identify more new features as the UCSF community begins to explore the refreshed CLE. In the meantime, LTG is here to help!

  • Attend a CLE Clinic for workshops focusing on new features and best practices. The Clinics are scheduled to begin again in September 2014.
  • Visit the CLE Support Center as we can continue to develop support materials for the CLE.
  • Provide feedback via the CLE Refresh Survey located on the front page of the CLE starting Saturday, August 2.
  • As always, contact the Learning Technologies Group with any questions!

Image Credit: “Refresh” designed by Andrew Lynne from the Noun Project.
Image Credit: Moodle Trust

Categories: Convergence

Using Mendeley for Collaboration

In Plain Sight - Thu, 2014-07-31 13:31

A new generation of citation/reference management applications are making it easier to share references and text with colleagues. This is the first of a series of posts looking at some of the most popular ones.

Of all current reference managers Mendeley probably stands out as a collaboration tool for researchers. Mendeley is a desktop and web program for managing and sharing research papers and discovering research data. Its social networking features facilitates collaboration among researchers through the creation of groups which allow you to collaborate with any member of the Mendeley community. In private groups, you may share and annotate a list of documents within your PDF organizer, allowing you to collaboratively tag and annotate research papers. In public groups, you may create a reading list with your colleagues and make it accessible to anyone on the web. Groups now also have an activity feed on Mendeley Web and in Mendeley Desktop, helping you stay up to date on new additions and discussions within the group.

View this short online tutorial explaining how to utilize Mendeley groups for collaboration:

 

 

 

 

 

 

 

 

Categories: In Plain Sight

Reminder: Collaborate Retiring August 2

Convergence - Thu, 2014-07-31 11:32

This is a friendly reminder that on Saturday, August 2, UCSF faculty, staff and students will no longer be able to create or join Blackboard Collaborate web conference sessions, and all recorded Collaborate sessions will be deleted from the UCSF Collaborative Learning Environment (CLE).

As part of the CLE Refresh, Blackboard Collaborate will no longer be supported at UCSF. Read more in the June 11, Convergence blog post Collaborate Retiring on August 2. WebEx is the web conference system supported on campus by the TeleHealth department.

If you would like to request a WebEx account or if you have general questions about using WebEx at UCSF, please contact Najla Faranza with the TeleHealth department at Najla.Farzana@ucsf.edu before your next UCSF course.

The Learning Technologies Group have been busy using WebEx in conjunction with the CLE for support and collaboration. The WebEx and CLE support document provides step-by-step instructions for adding WebEx sessions and recordings to CLE courses (click the image below to view the support document).

Questions?

Do you have innovative ways of using WebEx inside and outside of the classroom at UCSF? Please share them with the UCSF community in a comment below!

Image Credit: WebEx

Categories: Convergence

Bartholin’s treatises on snake poisons

Brought to Light Blog - Thu, 2014-07-24 11:39

As it’s the height of summer, that time of year when many of us head outdoors a bit more often, we thought we’d highlight a first edition from our rare book collection that addresses a potential hiking hazard– snake bites.

Dissertatio prima [et secuna] de theriaca in officina Christophori Heerford Sen. Pharmacop. was published by Matthias Godicchenius for Petrus Hauboldus in Copenhagen, 1671. The volume is composed of two dissertations on snake poisons and their antidotes, issued from the laboratory of two Copenhagen pharmacists. The manner in which Bartholin approaches the topic is of particular significance as it assumes that blood circulates throughout the body. He was one of the earliest advocates of Harvey’s theory of blood flow.

Thomas Bartholin was no slouch himself. He discovered the lymphatic vessels, contributed to anesthiology research, and came from an utmost scientific family that can boast pioneering work in the olfactory nerve, light ray double refraction, and discovery of Bartholin’s gland.

We hope you’re all enjoying the summer. Be safe and remember that even breeches and stockings may not protect you from everything.

Categories: Brought to Light
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