Tag Archives: education

ASMS 2018: Exhilarating and exhausting

The American Society of Mass Spectrometry annual conference represents my one sure visit to the United States each year.  What is it about this meeting that keeps bringing me back across the Atlantic Ocean?  What makes this gathering feel like an academic home?

Early Days

My first encounter with ASMS took place in 1998, when I attended the annual conference in Orlando.  During this and other early years of the conference, I made it my goal to eat only free food during the four days of the conference.  I remember ice cream breakfasts from a vendor at this first meeting!  Being notoriously frugal did my waistline no favors, but then I was skinny as a rail during graduate school.

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Prof. Pevzner, from his early days as a Wild West sheriff

My Ph.D. project involved the creation of a automated sequence tag inference engine from low-resolution tandem mass spectra of peptides.  That meant I had one particular talk on my agenda for ASMS 1998.  I listened with rapt attention to talk WOF 3:10 given by Pavel Pevzner (then a scientist at Millennium Pharmaceuticals) describing his SHERENGA software: “Automated De Novo Peptide Sequencing.”  I remember introducing myself to him after his talk.  When I mentioned my project, I remember poking in that we were competitors!  I was a frightfully competitive guy back then.  I am grateful that Pavel let the comment pass; in the two decades since that meeting he and I have become friends.

I feel I must mention ASMS 2004, the year that John Yates, III won the Biemann Medal, which I consider to be mass spectrometry’s highest award.  The conference was held at Nashville, TN, which was lovely given that I was a post-doc at Oak Ridge National Laboratory, just four hours down the interstate.  I arrived at the conference to learn that Steve Gygi, a friend of mine from graduate school, had played an epic prank on John and me at one of the preliminary meetings.  A student of his had captured a video of John and me encouraging people to get out onto the dance floor at a Keystone Symposium.  Steve had used the video in a research talk to show that while John was an expert in biochemistry, analytical chemistry, and bioinformatics, he couldn’t dance!

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…of which the less said, the better

Professional Integration

To attend a yearly conference is one thing, but becoming part of its organization is quite another.  After I joined the faculty of Vanderbilt University in 2005 as an assistant professor, I decided that ASMS was the organization that felt most like “home” to me, and I began paying my dues yearly rather than haphazardly on the years I planned to attend the conference.  I became familiar with a growing number of its luminaries, both through the senior scientists with whom I collaborated and through smaller meetings, such as the Association of Biomolecular Resource Facilities and the United States Human Proteomics Organization.  Happily, I gained a reputation as an energetic speaker who could make mass spectrometry informatics seem more approachable.

My three biggest public roles within ASMS have all been drawn from the field of mass spectrometry informatics.  I feel deeply honored to have twice selected the speakers to appear in panels on the informatics of identification.  My second big involvement was with the Bioinformatics Interest Group.  After the main panels on each full day of the conference, ASMS features workshops for interest groups, running from 5:45 to 7:00 PM.  Since the conference attendees tend to exhaustion after such busy days, the workshops function best when they feature passionate speakers that interact quite a lot with the audience.  I am certainly not ashamed to stand outside the meeting room, inviting absolute strangers to join our group!  I enjoyed my moments as Donahue, running between different members of the audience with the microphone.

My biggest engagement, however, has been a long-running ASMS short course.  In 2011, Alexey Nesvizhskii, Nuno Bandeira, and I offered “Bioinformatics for Protein Identification” for the first time.  In this two-day short course (on the Saturday and Sunday preceding the conference), we introduced the algorithms that enable protein identification for newcomers to proteomics.  Happily, the course drew a good response, and we have now run the short course for eight consecutive years!  It’s a lot of work, and it makes each ASMS visit six days rather than four, but I really draw a lot of satisfaction from working with the participants.

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The 2018 class

ASMS 2018: San Diego

What made this year such a busy program?  I would start with the fact that I completed my Ph.D. at San Diego, and I had many friends to visit while there!  I was very grateful to visit with friends from the “Darkstar” science fiction, gaming, yoga, and movie-making club; I hadn’t seen many of them for fifteen years!  I was also happy to see Ben Winnick, a friend of mine since my undergraduate years at the University of Arkansas.  It’s humbling to think I have known him since 1997.  These social calls complemented the professional friendships I was able to renew at the conference.

Since John Yates has made his home in San Diego since 2000, I was also glad to attend the reunion dinner he organized on the Saturday before the conference.  I was sitting down to dinner with my extended family of 200 friends, a bit worn out from running the first day of our short course, when I learned that the first speaker for the event had dropped out due to illness.  I was soon penciled in to replace him!  I frantically scribbled some notes while eating so that I could share some of my favorite stories from the early Yates Lab.  I was glad I could make people laugh!

Although I was not part of this year’s bioinformatics interest group, I was included as a speaker for the Analytical Lab Managers Interest Group under Emily Chen and David Quilici at their Monday evening workshop.  I emphasized the methods core lab managers need to incorporate “Big Data” into their work, emphasizing data repository use and careful statistics.  I slumped into my hotel bed directly after this talk; I had been yammering about something or other almost continuously for three straight days.

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Dave goes contrarian.

Wednesday put me right back on stage.  I was slated for a mock debate over at the Informatics Hub.  I was paired with my friend Juan Antonio Vizcaino (responsible for PRIDE repository); he would argue that Big Data was transforming proteomics, and I would argue that Big Data was creating more problems than it was worth!  It’s true that I have some doubts about the value of Big Data practices to date.  I hope my talk caused participants to think about good strategies for its incorporation.

Of course, the “work” that most conference attendees incur still awaited me.  I had submitted a poster reporting work I have conducted in agricultural proteomics with the University of the Western Cape.  We created an ortholog mapping table via BLAST that allowed us to determine which protein in sorghum mapped to which protein in maize.  We then used the mapping table to re-align our spectral count table so that the counts for each ortholog pair appeared on the same row.  This means our statistical model can look for differences between our “wet” and “dry” cohorts in both species, simultaneously!  I look forward to writing that paper.  My poster had been slated for Thursday, so I dutifully stood beside my A0 format poster throughout the morning and into the early afternoon.  I was glad to see that the poster hall was not completely deserted, even on the last day.

I am grateful to the people that launch the annual conference for ASMS each year.  It’s wonderful to gather with friends and see what each of us has created in the course of our work!

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Strolling the Heidelberg Altstadt

To visit a city with as much history as Heidelberg only to spend 100% of one’s time at a conference would be a great injustice. Between my wanderings on my arrival day and this evening, I have really come to appreciate the beauty that this city presents at unexpected moments.

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The lovely banks of the Neckar River

Heidelberg architecture begins its ascent in the twelfth century, with a local Benedictine monastery dating to 1130; the name “Heidelberg” didn’t appear in writing until 1196, though. Over a period of five hundred years, the Counts of the Palatinate and the Prince Electors resided in this city. A fortification on a hill overlooking the Neckar River was mentioned as early as 1303; today, this site is dominated by the ruins of a majestic castle!

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A schloss by any other name…

In many respects, though, Heidelberg gained fame as a center of learning. Prince Elector Ruprecht I founded the “Ruperto Carola University” in 1386, making it the oldest university in Germany. After an early 19th century reorganization, the institution came to play an even greater role, with luminaries such as Hegel advancing philosophy while Robert Bunsen invented gas-analytical methods (and inventing the Bunsen Burner) and Hermann von Helmholtz investigated visual perception.

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The old university plaza, featuring a tower from the nearby Jesuit church, was an ideal place to read a book!

For two decades in the early 19th century, Heidelberg became the focus of the “High Romanticism” literary movement. At the opening of the 20th century, the city constructed a palatial university library in the heart of its old town. In December 2014, UNESCO named Heidelberg as its tenth “City of Literature.”

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The library in the old town is tremendously impressive!

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Peterskirche

The churches of the city are really striking, as well. Peterskirche, the oldest, was originally constructed in the 12th century. Its tower almost seems like a post-modern deconstruction of a Gothic chapel, with flat faces in each cardinal direction and shuttered windows flush to the surfaces below its clock dials. I would have loved to explore its insides, but its doors were shut late on Tuesday afternoon when I visited.

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No nave is complete without a giant, reflective cross!

I also loved the Jesuitenkirche and its accompanying college. The church encompasses three parallel naves of equal height. I stepped inside and was delighted to see all the light pouring into the nave from the setting sun. I listened surreptitiously to an organist rehearsing for a service. I tried to set my phone down on a large table at the back so I could make an audio recording, only to realize that it was a fountain of holy water! I pulled it out of its damp case and got the recorder working properly.

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Springtime on Philosopher’s Walk

Learning that the “Philosopher’s Walk” led to a beautiful vista of the castle and old city from above on the opposite bank of the Neckar River, I began my walk up the slope. What I hadn’t seen mentioned is that the Philosopher’s Walk is steep. This middle-aged professor huffed and puffed, particularly on the initial parts of the ascent. After a while, the slope calmed down and I only needed to take care of the sun, which was beating down pretty well for a day in early spring!

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The Church of the Holy Spirit, as seen from Philosopher’s Walk

The climb was definitely worth it! I found a lovely flower garden at one scenic overlook, and the vision of the old city below was astonishing. To see the churches standing tall among the surrounding buildings helped separate them from the background. The castle’s architecture makes it seem like a fantasy rather than anything brooding. As I looked to the west, I saw modern Heidelberg spilling out along the riverbank. Heidelberg’s history, its legacy, and its charm make it a very appealing package.

You can be an academic YouTube STAR!

Many universities have begun exploring the use of the Internet for sharing academic coursework, either via “flipped classrooms” or Massive Open On-Line Courses (MOOCs).  Over the last year, I have uploaded approximately 50 videos to my YouTube Channel, most of them academic lectures.  I hope that I have learned something in this process that will you to publish your work more broadly, as well!

I would start by explaining that my lectures come from multiple purposes and even multiple university campuses.  My longest-running series of lectures came from a weekly seminar on topics of my own choosing called “the Useful Hour.”  I produced fourteen of these sessions (with help from Brigitte Glanzmann when I had to be away for a week), though I only started recording them on video for the last twelve.  I recorded the eight-session bioinformatics module from our division’s B.Sc. Honours program as a trial run for creating a “flipped classroom” in future years (a model where students watch lectures outside of class and spend in-class time working exercises).  More recently, I collaborated with the H3Africa BioNet to produce a four-lecture module on Gene Expression.  From time to time, I help the Tygerberg Postgraduate Student Council by recording a lecturer.  Each of these experiences has had its own lessons to convey.

The technical aspects of recording a video are generally easy enough that even a Ph.D. can do it!  Today’s budget camcorders capture more detail with better sound under lousier conditions than did cameras that cost five times as much even five years ago.  Best of all, one no longer needs to wrestle with tapes and analog-to-digital transfer loss.  Today we simply pull the Secure Digital card out of the camcorder and plug it into the socket on a laptop, where the video files are instantly accessible.  Of course, many people record video using digital cameras or cell phones.  Preparing videos for upload to a public server, however, is frequently more difficult than the initial capture.  I’ll talk about these aspects below.

Focus on the speaker

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Speak softly, and carry a big stick!

We must start with video that is worth watching.  Far too frequently, I see that people recording lectures focus on the slides rather than the person who is delivering the lecture.  Reading text from video is generally unpleasant, and the reality is that looking at people fires circuits in our brains that academic content does not.  Video is a format designed to capture motion; it is a notoriously inefficient method for capturing still images, though!  Keeping the camera on the speaker, then, makes more sense.  This comes with some caveats:

  1. Viewers still need to be able to see the slides.  My answer has been to produce a PDF from the PowerPoint or other presentation software, since almost everyone has the ability to view PDFs on any platform.  I post the PDF to a shared directory on Google Drive, and I include the URL leading to the PDF in the YouTube description.
  2. From time to time a researcher will point to a particular part of a slide.  This is probably problematic on video; if he or she has used a laser pointer, the spot of light will either be too bright (green) or too dim (red) to appear well on video.  A moving mouse pointer might be better.  If the speaker is old-school (like me), he or she may use a stick to point at the slide instead.  This can create a problem of the lecturer “blooming” as he or she moves away from the bright field created by the projector into the relative dark outside the projector’s light.
  3. How will a person watching the video know to advance to the next slide?  Hopefully the speaker says “next slide” out loud.  When my parents recorded my brother’s and my first efforts to read aloud, they told us to bang a spoon against a mug to produce an audible chime with each page turn.  That was even more fun than reading!
  4. Software is publicly available to integrate the slowly-changing slide video with the quickly-moving speaker video.  Screencast-O-Matic will produce videos of up to fifteen minutes in its free version.  This approach will guarantee that your viewers are seeing the same slide the lecturer is seeing as the talk progresses.
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Screencast-O-Matic insets your image atop the slides you are presenting.

Light and detail go hand in hand

As I alluded above, lighting is frequently a problem in academic lecture videos.  We frequently keep our lecture halls very dim in order to make the slides stand out as much as possible.  In a large venue, you may have a spotlight on the speaker, which will help.  In a medium venue, you may have a light in the ceiling directly above the speaker, which can make him or her appear somewhat ghoulish.  The more you rely upon zoom, the less light will reach your camera!  Keep that camera close.  If you can open the blinds on a window so that your speaker is lit, you will have a more interesting video.  Try to find ways to position your camera between the light and the subject (without casting a shadow, of course).  Never forget that the projected slides are much brighter than the subject you are trying to record.  If even the corner of the projected image appears in-shot, expect the speaker to become a flat silhouette.

Today’s cameras can record in very high resolutions, such as 1080p (the same as your HD television).  If lighting is truly problematic, you may want to consider forcing your high-resolution camera to a lower resolution, such as 720p; this may allow it to combine intensities across multiple transistors for each pixel.  Similarly, you should expect that a camera with a larger “retina” will outperform one with a tiny CCD in low light.  To put this in plain terms, do not expect a cell phone to produce quality video in semi-darkness, no matter the name on the label.  That said, I have observed that my “mirrorless” Canon EOS-M2 is inferior to my much cheaper Canon VIXIA HF R62 for video.  The lenses and electronics of the EOS-M2 are optimized for photos, not video.

Privacy issues are a big deal

Ensure that your audience knows that the lecture is being recorded.  Bad things can happen when a person does not want his or her image to be on-line and somebody else decides that they shall be.  Imagine how much worse this becomes when that member of the audience is a minor!  Nobody should be forced into public view because he or she attends a talk.

We frequently expect a period of questions and answers at the end of a lecture (and sometimes in the middle).  A novice camera operator may automatically swing to capture the questioner in action.  Depending on the situation, this part of the video may need to be truncated outright due to privacy issues.

Video is big and hard to handle well

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I use my hands a lot.

When I upgraded to my Canon VIXIA HF R62 from a JVC Everio (GZ-HM30AU), I had a rude shock.  My old camera had captured 720p video in very manageable MTS files, but the new camera captured 1080p video in massive MP4 volumes.  I used a 16 GB SDHC card for videos.  The cameras assumed that no file should be allowed to be larger than 4 GB (linked to 32-bit computing).  With the new camera, I consume 4 GB every 33 minutes!  At a couple of long events I recorded, I found that I needed more storage than the 16 GB card could provide.  I solved that problem by upgrading to a 64 GB card.

Naturally, keeping the raw footage of every event I video is not practical.  If each of the 50 videos I posted to YouTube over the last year produced 66 minutes of raw footage, I would need to archive 400 GB for just this period!  Similarly, posting these videos to YouTube would be a problem.  Each hour would span two files, which would require my viewers to watch part ‘A’ and then queue up part ‘B’ immediately afterwards; many would just skip watching the end, humans being humans.  To compound the problem, I live in South Africa, which means my upload speeds to network servers are dreadfully slow.  My home DSL line, for example, achieves 0.3 Mbps.  I have uploaded one GB before, but it takes hours.  In any case, I will probably need to truncate a bit of time off the front and the back of the video.  In short, I need to do video editing.

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While semi-professionals might opt for Adobe Premiere and those who “think different” will break out iMovie, I am a bioinformaticist, and I like software that lets me master high-quality videos with a minimum of fuss and bother.  I use ffmpeg, a very powerful suite of tools that one can use directly on the command line.  Most of the time, I am (a) concatenating my source video files into one movie, (b) including only a middle section, and (c) writing a more compact movie from the source materials.  To use a recent example, I have two input files; I write their names into a file called list.txt:

file mvi_0031.mp4
file mvi_0032.mp4

Next, I run a command line that looks like this:

ffmpeg.exe -ss 00:00:15 -f concat -safe 0 -i list.txt -t 00:50:00 -c:v libx264 -preset slow -c:a copy output.mp4

In order, the options do the following:

  • -ss specifies where in the combined files ffmpeg will start the output video (in this example, after the first fifteen seconds).
  • -ff concat -safe 0 -i list.txt specifies that the files listed in list.txt should be combined into one video and that they are formatted the same way.
  • -t specifies the total duration of the video to be encoded (in this example, exactly fifty minutes).
  • -c:v libx264 -preset slow specifies that my output video will be MPEG 4 pt 10, a very common format for storing video (and one that YouTube knows how to read).
  • -c:a copy directs ffmpeg not to re-compress the audio, making it sound just as nice in the output as it did in the original.

The ffmpeg software is very good at reducing the size of videos without compromising its quality.  I find that I can represent an hour-long lecture in a two GB 1080p video, rather than the nearly 8 GB of source footage.  If I am filled with caffeine for my lecture, the video size increases a bit (more motion requires more bits for accurate representation).

These smaller videos can then be uploaded to my YouTube account.  Happily, if you have a Gmail account (or if you use a different email address to log into Google Services), you can simply use that login for YouTube.  One clicks the arrow pointing up, and a screen will appear to which you drag your video file.  All done, right?

No job is finished until the paperwork is through!

Meta-data is key to your video reaching an audience, and too few people spend adequate time on this step.  I would call your attention to both the “Basic Info” and “Advanced Settings” pages that video authors can complete.  Of course, you should enter a paragraph of information in the basic description blank.  Ask yourself what web searches should find your video, and be sure you include those key terms in the text.  For good measure, add them again in the keywords section!  I like to include the university name where the recording took place.  Hopefully the social media minders for these schools will highlight your video to their large audiences.  YouTube will sniff the video for still frames that might be representative for the video.  I always try to pick the one in which I do not look like I’m suffering a fit of some sort.

Advanced Settings has more options to help users find your video.  Pick a category; generally my lectures fall in the “Science and Technology” category.  Be sure to enter a video location.  Google will translate your information to GPS coordinates so people can find videos shot near particular locations.  Enter a recording date, and select the language of your video (especially if you are not using English).

In many cases, you will have several videos that belong together as a set.  When I produced a short biography and four videos on Gene Expression for H3A BioNet, I also created a “playlist” that contained all five videos in the correct order.  Remember, if you can hook a viewer into watching one of your videos, you might be able to retain their interest for a few more!  Ideally, people will like your stuff enough that they subscribe to your YouTube channel, receiving a notification every time you post a new video.  You will be launched on your next career as a YouTube star!

Are you ready to start a molecular biology M.Sc.?

Professors receive a lot of requests from international students for admission to post-graduate training.  In South Africa, that training could be for “Honours” (a one-year course), an “M.Sc.” (a two-year Master’s program), or a “Ph.D.” (typically three years, post Master’s).  For students changing from one country to another, however, the question of “equivalencies” is key.  Could a four-year B.Sc. (Bachelor’s of Science) from Egypt, for example, be treated as the same thing as a three year B.Sc. followed by one year of Honours in South Africa?  This post gives an example of the questions I asked as I recently tried to determine the right level of admissions for an international student.

The international office for my university had declared that a student’s four-year degree was certainly equivalent to a three-year B.Sc. in South Africa, but it left to the department’s discretion whether or not Honours training was required before a M.Sc.  To support the department’s decision, I decided to build an interview from questions that would delineate the limits of the candidate’s knowledge.  I used the roster of topics for the Division of Molecular Biology and Human Genetics 2017 Honours as a guide.  I used the number of didactic training days for each topic as a weight:

Field Duration
Molecular Biology 8 days
Mycobacteriology 7 days
Biostatistics 12 days
Bioinformatics 8 days
Immunology 8 days
Cell Biology 8 days
Scientific Communication 2 days

I also gave some consideration to the M.Sc. project the student would pursue in my laboratory.  In this case, the work related to the reproducibility of mass spectrometry experiments.  After pondering before my word processor, I selected these questions for the candidate’s interview:

# Field Question
1 Cell Biology What biological processes are described by the Central Dogma of molecular biology? Walk us through each.
2 Biochemistry What do we describe with Michaelis-Menten kinetics?
3 Computer Science How does iteration differ from recursion?
4 Analytical Chemistry By what property does a mass spectrometer separate ions?
5 Medicine In HIV treatment, what is the purpose of a “protease inhibitor?”
6 Biostatistics What role does the “null hypothesis” play in Student’s t-test?
7 Medicine What type of pathogen causes tuberculosis?
8 Genetics What is the purpose of a plasmid vector in cloning? What features do such vectors commonly contain?
9 Cell Biology What cellular process includes prophase, metaphase, anaphase, and telophase?
10 Mathematics The log ratio (base 2) between two numbers is 3. What is the linear ratio?
11 Immunology What is an antibody, and what is its relationship to an antigen? What are the major families of antibodies?
12 Computer Science What is the purpose of an Application Programming Interface (API) or “library?”
13 Biochemistry What do we describe as the secondary structure of a protein?
14 Genetics Of what components are nucleic acids constructed?
15 Biostatistics What is a Coefficient of Variation?
16 Mathematics If I divide the circumference of a circle by its diameter, what value do I get?
17 Immunology What type of immune cell is the primary factory for antibodies?

The interview, conducted via Skype, lasted approximately an hour. As I asked each question, I gave the question orally and pasted the text of that question into the chat session. Remember that as an American, I have a “foreign” accent for the English-speaking population of Africa! I did not want that to be a factor in the candidate’s performance. I was grateful that our division’s Honours program coordinator, Dr. Jennifer Jackson, accompanied me during the interview, both to monitor that the candidate was treated fairly and to ask follow-up questions of her own.

Why did it take an hour to answer these questions? As is customary in post-graduate education, each answer opened the door to a series of other questions. A student may give an answer that covers only part of the question, and the follow-up will poke into the omitted area to see if it is an area of weakness, almost like a dentist with an explorer goes after a darkened area of a tooth to see if it represents dental decay!

Another factor that I want to measure for students is the degree of integration that they have achieved in their educations. To recognize that a word has been mentioned in class is not sufficient; I need to see that students understand how key concepts relate to each other. This synthesis is sometimes hard to evaluate, but it’s important. A student who doesn’t understand how a concept integrates with others will not be able to apply the principle or recognize when it should come into play.

Before the readers of this blog begin showering me with applications, I need to emphasize that the questions I framed for this particular interview are not the questions I would ask of another candidate. The ones above were chosen to reflect the background of the candidate, the diploma program to which he or she had applied, and the nature of the project I had in mind.

I hope that this post will help you decide whether or not you are ready to plunge into post-graduate education!

Teaching on the sly

When I first arrived at Stellenbosch University, I was a bit concerned.  I had thoroughly enjoyed organizing my own semester-long class in bioinformatics for M.Sc. and Ph.D. students at Vanderbilt University.  Under the “British System,” though, students encounter their final classes in the “Honours” year, crammed between the three-year Bachelor’s program and the two-year Master’s program.  Interestingly, a student may attend Honours at a different college than where he or she completed a bachelor’s degree, and the student may go to yet another university for a Master of Science after the Honours, so long as the training is judged to be relevant.

Overview of South African education program

This sequence describes the common route through South African education, from kindergarten to a terminal degree.

I would take a moment to explain a couple of important features here.  In South Africa, students are required to complete only the first nine grades, called “General Education and Training.”  In the United States, graduation from high school means that you have met your high school’s requirements for that goal (which in turn must meet state requirements).  In South Africa, however, high schools essentially serve to prepare students to take the “matric” exams, which are set (created) and marked (graded) nationally.  Matric successes or failures are what decide a student’s opportunities going forward.  I should also say that the chart above describes the academic track.  Many students take advantage of TVET (Technical and Vocational Education and Training) schools that lead to a certificate or diploma rather than a degree (these campuses have also experienced significant protests).  Each of these training types is considered in determining the SAQA level for a job candidate.

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The 2016 Honours class for the Division of Molecular Biology and Human Genetics

Students who come to Honours in the Division of Molecular Biology and Human Genetics (MBHG) may come from quite a variety of schools and backgrounds.  Like other divisions throughout Stellenbosch University and the University of Cape Town, we are trying to “transform,” or more faithfully represent the broader population of South Africa, and so we seek out candidates who may not have been able to afford the best schools for bachelor’s training.  Transformation is a hard task, and many universities are struggling [Note to self: read that overview chapter!].

My first exposure to teaching at Stellenbosch, then, was to create a bioinformatics “module” for our Honours students.  The group above got to serve as test subjects for my new curriculum, which spanned just four days in 2016.  Instead of 43 one-hour classes from my old Vanderbilt BMIF 310, I adjusted to four morning laboratories (each three hours) and four afternoon lectures (each two hours).  With so little time, I was obviously quite superficial in my coverage.  For 2017, though,  I will conduct a bioinformatics module that extends for eight days (during the first eight business days of May).  I am keeping the hands-on and lecture split the same as last year.  I think the doubling to eight days will be good for both the students and the professor!

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In this still from Useful Hour 3, Haiko, Michael, and I impersonate parts of a linked list.

Lecturing just eight days a year isn’t really satisfying my itch to teach, though.  This year I initiated a wildcat “course” of sorts.  The “Useful Hour” takes place each Wednesday at 1:30 PM.  Anyone on campus can attend, and we record videos each week for those who cannot.  The topics have generally been focused on computers, bioinformatics, or biostatistics, though in the coming week we will branch out into biochemistry, as well.  Since the Useful Hour covers so much terrain, I have tried to treat each segment as an independent story, with the topic for each Wednesday announced by my listserv on Monday.  It could be that the loose structure of the Useful Hour will cause its undoing, but for now I am really enjoying its playful vibe.

My work with the Blackburn Lab at the University of Cape Town on Tuesdays has led to another opportunity.  I have teamed up with Nelson Soares, a staff scientist, to create a monthly “Big Show” tutorial for the community of proteomics researchers throughout Cape Town.  Our recent program gave graduate students and post-docs the opportunity to present the essentials of protein identification and quantitation.  In April, we will look at the opportunities their acquisition of a SCIEX TripleTOF will confer on the group.  I appreciate that the students are also willing to listen to a lecture from me, from time to time!

The very latest teaching gig is one I hesitate to mention, since we are still formulating it.  In talking with more members of the Biotechnology Department at the University of the Western Cape, I’ve realized that they have a critical need for more biostatistics training.  I have never taught this subject formally, though I was part of the weekly “Omics” clinic for Biostatistics at Vanderbilt University for a few years.  Certainly one cannot function for long in genomics, transcriptomics, or proteomics without knowing something about biostatistics.  Teaching biostatistics formally is likely to teach me as much about the subject as the students who attend!  I hoped to use slides from Stellenbosch University for teaching weekly courses at UWC, but I could not get that use approved.  Instead, I have once again borrowed the expertise of my friend Xia Wang at the University of Cincinnati.  I am hopeful that I will be able to understand and use her didactic materials.  They’re written in the LaTeX math formatting language, so I will need to remind myself how to edit and export to a format I can display, like PDF. My last real experience with LaTeX was when I wrote my Ph.D. dissertation in 2003.

With students on three university campuses, I think I will finally feel like I have real some momentum in my teaching!

An extraordinary journey in three universities

Last November, I received some very welcome news.  The Deputy Vice-Chancellor for Academics at the University of the Western Cape informed me that I had been named an Extraordinary Professor in the Department of Biotechnology!  My work within that department had been going well, when persistent student protests closed the university through the end of 2016.  This letter reflected the ongoing hope of Biotechnology that our collaboration would continue when the students returned to their studies.  Today I received my official badge, so I would like to write about the work that is developing at each of the three local universities at which I have an appointment.

I have written about my travels among the campuses in and around Cape Town.  I would stress that I spend most of my time at my home institution, the Tygerberg campus for Stellenbosch University.  Bioinformatics has seen considerable investment by the university.  The South African Tuberculosis Bioinformatics Initiative represents the concentration of bioinformatics investigators for our campus: Gerard C. Tromp, Gian van der Spuy, and me.  There are other data scientists, though!  The Centre for Evidence-based Healthcare, led by Taryn Young, offers statistical expertise.  Tonya Esterhuizen specializes in biostatistics.  As I will explain in a moment, I hope to work with them more in the days to come.  This year, my formal teaching duties at my home campus will double.  Don’t worry for me, though, since I will host the Honours students for the Division of Molecular Biology and Human Genetics for only eight days!  I am glad that bioinformatics will have the “standard” module length for our Honours program, equal to Immunology and several other subjects.  I have been supplementing my teaching through an informal “course,” called the “Useful Hour.”  I have begun teaching all comers about a range of subjects, from computers to programming and statistics.  I hope to pull in some philosophy of science soon, as well.  I have been filming these subjects as a bit of an experiment, and it has been handy for those who cannot attend.img_20170126_152122

Hugh Patterton, Gerard Tromp, and I coordinate our efforts near Simonsberg.

The Stellenbosch campus of Stellenbosch University has made strides in bioinformatics, as well.  Hugh Patterton, a professor in the Department of Biochemistry, has been named to lead bioinformatics efforts at this campus.  Naturally, our group (SATBBI) has been talking with Hugh about ways we can reinforce each other’s efforts.  Some of our consultations on the Stellenbosch campus have pointed in the direction of microbiome research, an area that is replete with bioinformatics challenges.  I look forward to seeing what emerges!

I am highlighting the University of the Western Cape in this post, of course!  In describing bioinformatics at the campus, I should start by mentioning the South African National Bioinformatics Institute (SANBI).  Alan Christoffels leads this group of investigators.  They’re an interesting group, with considerable success in capacity development within South Africa and across the continent.  My home on the campus, however, has been with the Department of Biotechnology.  In many respects, this reflects how I have spent my career.  I set the mold in graduate school, when I was a bioinformaticist surrounded by analytical chemists.  I like being close to the people who generate the data I work with!  In the Department of Biotechnology, I work most closely with the group of Ashwil Klein, the lecturer who heads the Proteomics Research and Service Unit.  They have primarily emphasized a gel-based workflow, meaning that they partially isolate proteins on a 2D gel before identifying the spot based on the peptide masses they observe on the Bruker Ultraflex TOF/TOF.  The group is actively moving toward additional instruments, though, and the acquisitions should greatly broaden their capabilities.  I enjoy the intellectual challenges their group produces, since the rules of the road are somewhat less established for agricultural proteomics.

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The new UWC Chemical Sciences and Biological Sciences Buildings rise above the Cape Flats Nature Reserve.

In attending the department’s recent strategic retreat, I was introduced among the researchers of UWC Biotechnology more broadly.  I was particularly glad to meet with Dr. Bronwyn Kirby, who heads the Next Generation Sequencing Facility.  We discussed the Honours course offered for the department (I taught bioinformatics for the proteomics module last year), and I believe I’ll get to add some bioinformatics for the sequencing module in 2017!  I was also delighted to meet the SARChI chair who heads the Institute for Microbial Biotechnology and Metagenomics (IMBM), Marla Trindade.  We spoke about what the students of the institute most needed, and establishing a structured curriculum for biostatistics seemed very high on the list.  I mentioned the biostatistics researchers at Stellenbosch above.  My hope is to be able to use much of the structure Stellenbosch has already built in its Biostatistics I and II classes as a model for teaching biostatistics at UWC Biotechnology.  It would be my first effort at teaching biostatistics formally; I hope that I have absorbed enough to be a good teacher for this subject!

I continue to spend my Tuesdays with the University of Cape Town medical school and to visit the Centre for Proteomics and Genomics, as well.  UCT named me an Honorary Professor in the Department of Integrative Biomedical Sciences halfway through 2016.  My interactions there have principally taken place within the Institute of Infectious Disease and Molecular Medicine (IDM), borrowing from the network of relationships that Jonathan Blackburn has established there.  I have worked with Nelson Soares, his Junior Research Fellow, to create monthly programs for the Cape Town community invested in proteomics.  This Tuesday, we started this series for 2017 with an introduction to the methods we use for identifying and quantifying proteins.  I was really pleased that Brandon Murugan, a senior graduate student in the Blackburn Lab, felt comfortable enough to present this material!

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I enjoyed my sundown cruise with the SATVI team in May of last year!

From the very beginning of my time in South Africa, I have been working with the South African Tuberculosis Vaccine Initiative (SATVI).  Recently they began having their research in progress meetings on Tuesday morning, allowing me to take part.  I really like the interaction.  They take my questions seriously, and I think we all learn from working together.  Certainly I would find great meaning in being part of a successful vaccine trial for this disease!

I have another group I must mention in describing bioinformatics across these three universities.  Nicola Mulder’s “CBIO” team has been an opening wedge in bioinformatics education for South Africa.  Their H3Africa BioNet courses have been used to supplement the content of B.Sc. education in places like the University of Limpopo.  It should be no surprise that many of the people I have mentioned in today’s post have collaborated in a manuscript describing the growth of bioinformatics in South Africa.  Our field is key to the future of public health and to the advances in biotechnology yet to come!

In search of diamonds at Kimberley

In the Northern Cape of South Africa, the Square Kilometer Array has partnered with Sol Plaatje University to produce an annual “Big Data Careers Day” for the undergraduate students in the Data Science degree program.  I was very fortunate to be included in this year’s program (courtesy of the Newton Fund) to explain the field of bioinformatics to these learners and invite them to consider graduate study in the field.  In the late 19th century, Kimberley was a place where we scoured the earth for diamonds.  Hopefully the 21st century will be the era when its young people become diamonds through education.

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Vice Chancellor Yunus Ballim (SPU), Bonita de Swardt (SKA), and I were all smiles after a solid first day.

“Data Sciences” spans a considerable number of subjects, ranging across mathematics, statistics, and computer science, to prepare graduates for work in “Big Data.”  Because the Square Kilometer Array is under construction in the Northern Cape, 400 km to the southwest of Kimberley, many of these students hope to become engaged in astronomy research.  Major technology companies, such as Google, IBM, Dell, Microsoft, and Cisco, made their own pitches for the students, as did local Big Data institutions, such as Tracker, the Centre for High Performance Computing, and other universities.  I focused my message about bioinformatics on four key points:

  • We make a difference in confronting public health menaces, like TB and HIV.
  • Our careers let us pivot to new application areas at will.
  • Academics travel to many places in attending conferences and invited talks.
  • Graduate students in the sciences receive funding to cover costs during training.

Even though I was near the end of a long day of presentations, I felt that the students resonated the energy I put into my discussion.  Several of them expressed interest in practical internships or even attending honours at Stellenbosch Faculty of Medicine and Health Sciences.

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What a great group!

On the second day, I went in search of diamonds of a different sort.  I visited the town’s premier tourist attraction: The Big Hole.  When diamonds were discovered in 1871 on the De Beers farm, the area was a small hill.  After thousands of would-be prospectors acquired rights to mine small claims, the soil disappeared quickly.  By the time the mine had closed in 1914, the wealthy town of Kimberley had begun the industrialization of South Africa.  A massive “headgear” had been constructed to haul loads out of the mine.  A staggering 2722 kg of diamonds had been taken from the ground, with tunnels stretching as far as a kilometer below (essentially the same as the height of Table Mountain above sea level).  This is what remains of that hill:

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For scale, the distance from the surface of the water to the ground outside the excavation is 175 m.

In the mid-1900s, the city of Kimberley decided to turn this site into a history museum, and they relocated many historic buildings to a preserved village on the northwest corner of the hole.  My walk to that village passed through the downtown area, but I soon saw I had taken the wrong route; a high gate with razor wire surrounded the hole, and the area was heavy with litter and an unpleasant smell.  I turned south to walk through the largest concentration of taxi mini-busses I have ever encountered.  I endured my nightmare without screams and continued on my counter-clockwise route around the crater.  After passing a revivalist church of excitingly modern architecture, I reached the entrance to the historic village.  The headgear still stands above the observation platform.  I was heavily reminded of the structure appearing in Buffy the Vampire Slayer Season 5 during the final episode.

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The head gear dwarfs the buildings around it.

The village itself is an interesting collection of old and new.  I was particularly interested in a church (constructed in 1875) and a modular home that was prefabricated in England (1877) and then ported by oxwagon from the coast to Kimberley.  Inside the church, old recordings of hymns are played.  It’s a little spooky, honestly.

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Rapid construction is not always beautiful construction, but these buildings have endured quite well.

One of the biggest surprises for me came from one of the tallest structures in the historic village, with a lovely spire above it.  I saw that it was closed because a class was taking place.  When I peeked through the window, I saw that a Butlers Hotel School occupied the ground floor.  The hospitality workers of tomorrow were learning their skills in a completely up-to-date kitchen!

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Electric lights! Electric street cars!

For me, this reinforces one of the key lessons of my trip to Kimberley: the true riches that we have in our cities are the people who live there.  I am excited to see so much effort given to training the next generation of South Africans.