Tag Archives: science

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.

IMG_7451

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!

Useful Hour 3

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!

Bang for the buck: U.S. aid to South Africa

Out of $4 trillion dollars in the U.S. federal budget, how much is spent on foreign aid?  While most people in a recent poll thought it was around a quarter of the annual budget, the true answer is around one percent.  In this post, I want to explain two key programs that have impacted my new home country: PEPFAR and AGOA.  The United States plays a substantial role in making the future of South Africa brighter!

PEPFAR: Curtailing the epidemic of HIV/AIDS

pepfar

During the first eight years of the millennium, I rarely had anything positive to say about the President of the United States.  President George W. Bush, though, signed into law the “U.S. Leadership Against HIV/AIDS, Tuberculosis, and Malaria Act of 2003,” which transformed medical care in southern Africa.  His name is still respected in South Africa because of this law; it yielded the President’s Emergency Plan for AIDS Relief (PEPFAR).  This program has been renewed twice by bipartisan vote, in 2008 and 2014.  In the thirteenth year of the program, PEPFAR supported anti-retroviral treatment (ART) for 11.5 million people living with the Human Immunodeficiency Virus (HIV), with that number having climbed by 50% since 2014.  Some two million babies have been born without HIV from mothers who carry the virus.  This is an amazing accomplishment, and it couldn’t have come at a more critical time.

The HIV crisis in South Africa began as it did in the United States, with AIDS appearing in the community of gay men during the early 1980s.  Cases were documented in the heterosexual community in 1987.  By 1990, the crisis had begun to grow rapidly.  It is worth noting that South Africa was coping with tremendous changes during this period as the Apartheid government was compelled to cede power; Nelson Mandela was released from prison in February of 1990.  When he became President in 1994, however, the new government was unable to do much about the growing epidemic.  1996 was a watershed year for HIV as ART was announced, and the first drugs became publicly available (though expensive).  In 1999, Thabo Mbeki was elected President, and the public thought that HIV prevention and treatment might become a priority under his leadership.  His Presidential AIDS Advisory Panel, however, was dominated by HIV denialists / “AIDS dissidents” who claimed the virus had nothing to do with AIDS.  Not only were ART drugs not made available widely, but ART was withheld from pregnant women carrying the virus.  Nelson Mandela re-entered the debate in 2000 by a powerful closing speech at a Durban international conference on AIDS.  The topic became even more personal to him when his son died of AIDS in 2005.  Against this complex historical background, the prevalence of heterosexually transmitted HIV-AIDS was surging.  “By 1994, this had risen to 7.6%, and by 2005 was 30.2%, with an estimated 5.5 million of South Africa’s 47 million people infected.  An estimated 1000 new HIV infections and 900 AIDS deaths occurred each day” [Giliomee and Mbenga, p. 418].

PEPFAR has a tremendous role to play in today’s South Africa.  The program currently estimates that 7,000,000 people in the country are living with HIV, with approximately half protected by ART.  180,000 people die of AIDS each year in South Africa. “South Africa now has the largest number of patients on anti-retroviral drugs in the world, and South African life expectancy has increased by more than a decade.” [Bekker et al.]  Just imagine the impact if PEPFAR were no longer paying for HIV treatment!

Please be aware that there have been changes in the Trump Administration that suggest this program may be in trouble.  It is no exaggeration to say that real people will die without PEPFAR.

AGOA: “Trade, not Aid!”

agoa-feature_1

Debate may never end over the best way for wealthy nations to support the growth of poor nations.  When wealthy countries give food aid to poor nations, those efforts can undermine the economic growth of agriculture in those countries.  The African Growth and Opportunity Act (AGOA) was enacted in 2000, the last year of Bill Clinton’s presidency.  You may be thinking, “gosh, another economic treaty I need to know about!”  In fact, AGOA is not a treaty.  AGOA is a unilateral decision by the United States to drop taxes and quotas on imports of particular goods from countries in sub-Saharan Africa.  The program began by including 34 countries and soon expanded to 40.  After the first fifteen-year run of the program, the U.S. Congress decided to renew AGOA for an additional ten years in 2015.  Each year, the President decides exactly which countries will be extended these benefits.

The metrics for AGOA success paint a somewhat equivocal picture.  The 2016 biennial report shows $23.5 billion in exports from Sub-Saharan Africa in the year 2000.  This number grew to $86.1 billion in the year 2008 before falling back to $18.5 billion in 2015.  This might seem an abject failure, but much of the decline reflects reduced oil exports to the United States and the worldwide recession of 2009.  Most Sub-Saharan countries, of course, would like to export to the world’s biggest economy!  America, in turn, uses this desire to requiring development toward “a market-based economy; the rule of law, political pluralism, and the right to due process; the elimination of barriers to U.S. trade and investment; economic policies to reduce poverty; a system to combat corruption and bribery; and the protection of internationally recognized worker rights” [2016 biennial report, p. 8].  Essentially, the United States waives taxes on imports from countries that behave as the United States would like to see.

South Africa has had an interesting story within the framework of AGOA.  As the continent’s most advanced and diversified economy, South Africa was a bit of a question mark for inclusion in the 2015 renewal of the law.  Did it make sense to give these trade benefits to an economy that was already moving rapidly?  South Africa made itself a less attractive trade partner by raising trade barriers against American farmers exporting meat to South Africa, which caused them to violate the “elimination of barriers to U.S. trade” rule above.  At the start of 2016, the situation had deteriorated enough that Barack Obama suspended AGOA benefits for South Africa.  This action was enough to convince the foot-dragging South African government to drop its trade barriers, and so South Africa is once again an AGOA beneficiary in good standing.

What will happen to AGOA under the Trump Administration? Although President Trump has been ambivalent on the subject of free trade, he has not signaled that he will seek to end AGOA either by unlisting all participant countries or seeking the repeal of AGOA through the Congress.  Africans do not expect great things from President Trump, though.  His Tweets about South Africa have had a generally negative tone.

In the end, South Africa is proud of its ability to take care of its own problems.  If AGOA comes to an end, the country will lose one of its best customers for fruits and vegetables, and the automobile industry growing in the Eastern Cape would suffer.  The loss of PEPFAR, on the other hand, would devastate health care in South Africa.  The economy of South Africa is not strong enough to bear the cost of supporting ART on this scale.  The country already relies on the permissive, pro-public health intellectual property laws of India to have access to generic ART.  We can all hope that the PEPFAR and AGOA relationships between South Africa and the United States continue under President Trump!

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.

img_5457

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!

img_2949

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!

With the new year, a new office!

The Division of Molecular Biology and Human Genetics occupies the fourth floor of the FISAN building at the SUN Faculty of Medicine and Health Sciences.  As its research programs have become better funded, substantial numbers of clinical and research staff have been added to its roster.  One practical result of this addition was that I shared an office with three other researchers when I arrived in South Africa in late 2015.  With the start of 2017, however, our division has gained access to office space on the third floor.  I am happy to report that as of last week, I have a new solo office!

This move does not come without regrets, though.  I have become friends with the inhabitants of F416, and my new hallway currently seems quite lonely by comparison.  Sam Sampson is a group leader who came to SUN via the National Research Foundation “South African Research Chairs Initiative,” and she has impressed me with her concentration skills in our busy office.  I also appreciate her thoughtful gift of teaspoons when mine went missing!  I really value Kim Stanley’s friendship; she has been very tolerant of my practical jokes, and occasionally I catch a glimpse of her mischievous sense of humor.  She invests countless hours in the REDCap study databases that undergird much of the research for our division.  Nasiema Allie was the last of the four people in our office to arrive.  Her job is quite critical since she ensures that the BSL3 lab facilities for our division are as safe as they can be.  Why is that a big deal?  Our division emphasizes research in tuberculosis, and we culture Mycobacterium tuberculosis from patient samples.  Some of the strains we recover from patients are resistant to every drug available to treat this disease.  Let’s just say that I don’t store my lunch in the freezers lining the division’s hallways!

img_6413

Our freezers are equipped with wireless boxes that “phone home” if the temperature inside rises.

My new digs are on the wing extending east from the FISAN entrance.  To be on the third floor means I am several feet closer to the flock of chickens at ground level.  When I open the window (!) of my new office to feel a sweet afternoon breeze, I also get to hear the crowing of the roosters.  Last week we also had the questionable benefit of being closer to the smell of decomposition as cadavers were moved downstairs; FISAN is an Afrikaans abbreviation for “physiology and anatomy!”  That said, the third floor has great accommodations for the bioinformatics and biostatistics students we will be training in SATBBI.  The student chamber we have selected has abundant space, featuring bookshelves, a chalkboard, a bulletin board, and even a sink!  Right outside we have a smaller area we hope to position as a meeting room.

img_6406

We haven’t reached our final configuration for the desks in the bioinformatics student workspace.

This brings us to my office.  I was one of the first professors to pick out my new home, and I decided on one featuring a blue wall (rather than the beige featured throughout the complex), an intact chalkboard (rather than the removal scars from one that had been removed), and a ledge underneath its narrow window.  I discovered that the ledge was the perfect height for tucking a cabinet or drawer set from our old furniture upstairs.  They will match the desk that my graduate student and I hauled downstairs from my old office.  The ledge is sturdy enough that I can stand on it to raise my window, so I feel confident that it will house some plants for me soon!

img_6410

All I need now is a coffee table.

Moving my computers down was a bit more worrisome.  Happily, the LAN port (or “network point,” as they would say here) was already live, though it is a slower 100 Mbps rather than gigabit.  In any case, my Ubuntu Linux file server “Deep Thought” made the transition downstairs without a hiccup.  I recently brought my Intel Core i7 workstation “Alabaster” from home; it connects to the network wirelessly, so I can use a network wire to connect the two computers in my office directly.  Using a gigabit network port exclusively to communicate between the pair means I can use the RAID from Deep Thought almost as though it were a local hard drive in Alabaster.  This may be as good place as any to mention an act of generosity from Vanderbilt University.  When I decided to move my lab to South Africa, the Department of Biomedical Informatics allowed me to move almost all the computers associated with my laboratory to Stellenbosch University!  It made a real difference to my new division.

img_6422

What office is complete without a memento or ten?

I have assembled a collection of treasures on my desk that link me to my past.  Probably my oldest memento is a koosh ball that I acquired in high school.  I am very fond of my jar of marbles for my discussions in frequentist biostatistics; I bought these marbles when I was starting as a professor at Vanderbilt from the Moon Marble Company, near Kansas City.  My first Ph.D. graduate student bought me a jade pen holder that I use everyday.  My singing bowl from China gets a special place of prominence.  A small, red Buddha was a parting present from the Harkeys, close friends from Nashville.  An analog clock from Vanderbilt reminds me of my friend Bing Zhang, who headed to Houston around the time I moved to Cape Town.  I don’t remember where my Ganesh came from, but he has a reputation for finding the solutions to problems, so he definitely belongs on my desk!

My name placard has moved, I have given up my key to F416, and all my things have migrated downstairs.  Over the weekend, my lovely girlfriend bought me white and colored chalk for my new chalkboard!  Now it’s time for the science to flow from my desk once again.  Wish me luck!

img_6408

This hallway awaits the rest of its occupants!

 

Semmering, Austria: Proteome Informatics on the upslope

At the start of 2015, I was incredibly fortunate to attend the Midwinter Proteome Informatics Midwinter Seminar at Semmering, Austria.  Although I did not initially know many of the participants, I have subsequently become friends with many of them.  In some cases, we have even written papers and grants together!  I was thrilled to return to Semmering on January 8, 2017 to attend a sequel to this meeting, this time sponsored by the European Proteomics Association.  Our group had nearly doubled from fifty-six to one hundred and five!

dsc02635

January 14, 2015 (Schneeberg appears in the distance behind us.)

img_2229

Jan. 11, 2017 (photo courtesy of Marc Vaudel)

Despite its small population (below six hundred permanent residents), Semmering is actually an interesting place.  The town is named for the eponymous pass through the Northern Limestone Alps.  The area gained special prominence in 1728 when Emperor Charles VI of Austria completed a road over the pass, a feat commemorated by a hefty monument near the ski resort.

img_8257

The 18th century monument bathes in the Zauberberg night lights.

One hundred twenty years later, the pass served as a key railway connection, tying together “Lower Austria” and Styria, one of the nine federated states of Austria.  The stylish and well-engineered construction of this railway has been listed by UNESCO as a World Heritage Site.  The railway reaches almost 900 m above sea level.  The tracks employ tunnels and graceful bridges through a ruggedly beautiful terrain.  These rail links accelerated development in the area, making Semmering a major resort destination.

Our conference had grown so much in size that we occupied almost the entirety of the Semmering Sporthotel.  A feature that I particularly enjoy about this conference is the chance to create new tutorials for a crowd of advanced researchers.  In 2015, I premiered a half-day workshop on the subject of algorithms to identify post-translational modifications.  I asked this year’s organizers what kind of tutorial they would most like.  They responded by asking what I was working on right now.  I described my work in preparing sequence databases for identifying proteins of non-model organisms, starting from RNA-Seq experiments.  They replied that this would be just great.  I found it was a very useful exercise to learn the individual methods well enough to teach them to others.  In the end, approximately 35 students worked through the resulting half-day tutorial.  We were pretty challenged by the weak Internet service at the hotel, split across so many users, but most of the crucial steps were possible with data I had provided via USB drives.

mail

My diagram of extant search engines from two years ago

Two years ago, I had chosen a somewhat controversial topic for my plenary lecture (one given to all the attendees at once rather than a subgroup).  In “The Hard Stuff: MS Bioinformatics Moves Beyond Protein Identification,” I argued that the era of publishing new database search engines for proteomics was drawing to a close, since more than thirty such tools have now been published!  I urged them to look beyond these basics to find challenges in non-conventional identification: MS/MS scans containing evidence for multiple peptides, proteins that vary in sequence from a database reference, and peptides bearing complex modifications like glycans or non-ribosomal peptides.

mail

A banner image from my 2013 review of quality control

This year, I decided to spend some attention on a question of importance since I am chairing a quality control working group for the HUPO-PSI.  What types of biological mass spectrometry are not well-served by existing quality control approaches?  I discussed some of the existing efforts in quantitative mass spectrometry within Spectrum Mill, SProCop, and MSstats.  I contrasted this situation with the emerging fields of data-independent acquisition, in which superior reproducibility is regularly claimed without metrics that could substantiate those claims.

dsc02619

Jan 13, 2015: Johannes Griss and I discover our shared sense of humor. (Photo courtesy Lennart Martens)

With two meetings at Semmering under my belt, I must say I am hooked.  These meetings remind me of the lovely RECOMB Computational Proteomics meetings at UCSD from 2010 to 2012.  The quality of attendees is really substantial, and the free-wheeling conversations are highly entertaining and educational.  I must also say that there is nothing quite as thrilling as sledding down the designated path of the ski slopes head-first (NOTE: this posture is discouraged), the way I lost my lens cap in 2015!  If you are in our field, I hope I’ll get to see you at a 2018 meeting!

20170112_181605

Johannes Griss introduced me to Almdudler, a lovely tonic that is the taste of Austria for me.

Berlin: Travels upon travels

Less than two weeks after my return from Beijing, I was back at the airport.  This time my destination was Berlin, Germany!  This new journey had been set in my calendar long before, since it marked the final annual meeting of an international consortium.  The Bill and Melinda Gates Foundation had invested thirteen years of funding in our tuberculosis biomarker project.

Though I have been to Europe several times, I had never been to Berlin.  My first trip to Europe, a semester abroad during my junior year of college (late 1994), included a grand clockwise tour of the continent via Eurail, starting from Paris, France.  My original plan had been to leave from Dresden (airport code EDDC on the map) to head north to Berlin, but I… well, I chickened out.  I told myself that I was trying to avoid election day crowds, but actually I was just trying to cope with my fear of large cities.

map

My 1994 tour of Europe (courtesy of gcmap.com)

Getting to visit Berlin for work would help me patch that hole in my 1994 trip.  I also decided to take this opportunity to visit Warsaw, Poland; in 1994, I had seen only Krakow, which acts as something of a cultural capital for the country.  My favorite part of the 1994 cycle was seeing Eastern Europe.  In fact, the Cold War ended for me on the day that I visited Prague (LKPR).  A local college student showed me the Prague subway and explained that it had been driven deep into the earth so that it could serve as a fallout shelter when the Americans nuked the city.  It changed my view to learn that they had been as terrified of us as I had been of them.

common_face_of_two_euro_coin

I think this is my favorite coin in the world. It’s easy to spot in your wallet, and you can buy something substantial for it. (WikiMedia)

Getting to Berlin was reasonably straightforward.  I used an overnight flight from Cape Town direct to London Heathrow.  Then I took the shorter hop from London direct to Berlin.

Tegel airport in Berlin (TXL) is disappointing.  It seems like a relic from another age.  The first commercial flights (from Air France) began using this airport in 1960.  That said, it is very quick to navigate, since one can walk the entire hexagon in twenty minutes.  Berlin will have a new airport as soon as the end of 2017, south of the city center.  I left the airport by way of a city bus that could take me directly to the hauptbahnhof (main rail station), where my hotel was located.  It’s nice to be able to get from an airport to my hotel for only 2.70 Euros!

Our meeting took place at the Max Planck Institute for Infection Biology.  This Institute was created in 1992 on the grounds of the university hospital Charité (its services date back to 1710, during a bubonic plague epidemic) to improve the basic research capabilities of the former German Democratic Republic (“East Germany”).  I have really enjoyed our interactions with the bioinformaticists at this site.  January Weiner has constructed some pretty cool pipelines for handling data, even unfamiliar types like metabolomics data.  Helpfully, he was also able to share some suggestions to improve my trip to his native Poland.  His colleagues Gayle McEwen and Jeroen Maertzdorf have also impressed me with their thorough and careful analysis of metabolomic and transcriptional experiments.

img_6850

January speaks with Jayne Sutherland from the Medical Research Council in the Gambia.

Our research meeting had an unusually emotional tone.  The “GC6” team (Grand Challenges Six) has been in action since 2003.  Thirteen years is considerably longer than most collaborations stay together (I enjoyed nine years with NCI CPTAC, by comparison).  The effort has produced a considerable number of publications, Ph.D.s, and spin-off grants.  Some of its graduates now serve as co-investigators, actually.  The effort touches a large number of countries: the United States, Germany, Denmark, the Netherlands, the U.K., South Africa, the Gambia, Ethiopia, Uganda,  and Malawi.  I was really glad that everyone was game for a group picture.

img_6856

The GC6 team enjoys a chilly autumn afternoon outside.

In upcoming posts, I will describe my tourism connected with this meeting, but I do not want to start a travelogue without remembering the work that brought me to Berlin!

China: Shanghai Proteomics and the Qibao Ancient Town

An index to the China series appears at the first post.

September 28, 2016

I was glad for a relatively slow start this morning. I went for breakfast at the hotel, and the lady cooking eggs produced some lovely scrambled eggs for me. While I had been frustrated that I could not plug my laptop into the outlets at this hotel (unlike at WuKe) because the ground pin on my U.S. plug did not have a corresponding hole, I awoke with the realization that I could use my three-pin US to two-pin European converter to let me charge my laptop. Today was looking up!

Jing Li, my host at SJTU, arrived to pick me up at 9:15 AM, and she drove me around the campus. We stopped at a coffee shop that could have been anywhere in the world. I happily sipped my hot chocolate while she updated me on her progress in academia. I think she has found a great academic home. From there, we drove to her office. I like that many of the graduate students for the department of Biostatistics and Bioinformatics are seated right outside the offices of the junior faculty. I suspect that Jing Li will soon take her place upstairs with other senior faculty, though!

Minjia Tan, a rising star in proteomics, soon arrived at campus from the Shanghai Institute of Materia Medica (Chinese Academy of Sciences). He and Jing have formed a very effective partnership. He had many interesting questions on the relative merits of spectral count and peak areas for quantification of proteomic differences. We talked about some of the interesting challenges that have arisen in his research. Soon, he, Jing Li, and I headed over to the faculty club to have some lunch. I had a yummy combination of needle mushrooms and portobello mushrooms in brown sauce. Our conversation was a really interesting one. I learned of a multi-site investigation into proteomic reproducibility here in China, but the work has yet to be published. I hope I can help accelerate the process of its publication, since I have taken part in several such studies before. People need to know that proteomics in the developing world is viable and reliable.

img_6458

I had not realized how much I use my hands when speaking.

Before we knew it, the time had arrived for my talk! We drove back over to the Life Sciences building for my talk. Again I told the story of the CPTAC collaboration’s drive toward publications in three projects I helped to lead. This time, however, many graduate students were in the audience. I enjoyed talking to them directly about the challenges of reaching the first publication. Many students seem to feel alone in how difficult it can be to get a first manuscript accepted by a journal, so I really wanted to let them know that the process is challenging for everyone!

img_6463

This team asks good questions!

Soon afterwards, three of the graduate students squired me over to the Qibao old town (the name means “seven pieces of treasure”). We wandered through the village, taking in the sights. I saw a smaller road leading away from the heavily touristed area, and we followed it to some more specialized shops. The first was a gemstone store. It featured some very pretty almost feathery shapes in a distinctive green color. The Chinese name translated to “peacock mineral,” which we later discovered is called “malachite.” A second shop included jewelry of various sorts. I used the opportunity to ask a question that had been bothering me. Why walnuts? The owner explained that walnuts absorb lipids from our skin, making our skin appear healthier. As we began returning to the tourist area, we heard a strange scraping noise coming from one of the shops. It was a carpenter, applying a plane to some bound wood. He was creating a smooth planter for sale. Seeing the curls of wood come away from his planing was very therapeutic.

img_6498

This was once a massive pawn shop!

We continued deeper into the Qibao, across the River Puhui. We came to Fuqiang Street. Cricket House stands in memory of this quarter’s history in cricket fighting. We continued over to Yutang Street, where we took pictures at the massive three-story pawn shop.

When we turned back toward the river past Beigu Lane, we encountered a fascinating little second-hand store. I was excited, because I had been looking for just such a place since arriving in China. We looked through the books and found more copies of the Selected Works of Mao Zedong, but no 1960s copies of the little red book. As we worked our way around the shop, we suddenly found some very tiny red books. One of them was an ID for a plastics factory from 1980, apparently for the woman who ran the shop. The other was a small manual on the responsibilities of people who join the Communist Party. I was elated to discover it dated from 1969, the same year as my copy of the Selected Works of Mao Zedong!

img_6504

I am so grateful that she was willing to share these books with me!

With our spirits running high, we walked in the direction of the Qibao Temple. The sun was westering, and the skies began dripping a bit. When we arrived at the ticket office for the temple, the attendant announced that ticket sales had come to an end and commented that it was a temple, not a tourist site. I tried to keep a respectful mien; I have no desire to be “that American.” We returned to the tourist area.

img_6484

The sound of running water is blissful for me.

We paused by a restaurant where the chef was rolling noodles out by hand in the front window. The nameplate for the business read “Da Da Handmade Noodles.” This staple is a specialty of the Sichuan area, and the whole group wanted to taste them, so we ordered bowls for each of us. I must say that my chopstick skills are fairly rudimentary, and the weight of the noodles was a significant challenge for me. The grad students gave me some pointers on the placement of my fingers, but I mostly made my way by levering the end of a noddle out of the broth and sucking it the rest of the way into my mouth. Happily, making a slurping sound over your soup is expected.

img_6513

I am hungry all over again.

I was not anxious to leave my last night of tourism behind. The graduate students and I walked down the street. Jinqiu Xiao spotted a cart full of bootleg DVDs and asked if I were interested. I looked through the titles and found a likely set:

  • X-Men Apocalypse
  • Ghostbusters: Answer the Call
  • Captain America: Civil War
  • Star Wars: The Force Awakens

We asked the price, and the dealer replied 40 Yuan (divide by six for dollars). I pushed for the best price, and she said I could add a movie at that price. I added “Cobain: Montage of Heck.” Sold! (Remember, though, that giving money to bootleg DVD manufacturers supports the violation of U.S. law.) With my last memento purchased, we hailed a taxi and returned to campus and then the hotel. My time in Shanghai was at an end.

img_6495

Each red ribbon is a wish. I know I wish to return to this place!