Gas station without pumps

2014 October 2

On senior theses

Filed under: Uncategorized — gasstationwithoutpumps @ 10:07
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Today is the first day of classes for us, but I’ve already been busy advising both new and returning students. Last week I sent out an e-mail message to the bioengineering and bioinformatics undergrads explaining the senior capstone options. I’ll probably have to send out a similar message each fall, so I thought I would save it here, where I can find it again.  It also might be useful for students and faculty elsewhere, as a lot of the advice is generic for any student starting a research project, though some is specific to our program and even to this year.
A lot of bioengineering seniors are starting senior theses now, a few bioinformatics seniors are, and most juniors will be spending a fair amount of time this year looking for a lab or a senior project, so I thought I’d address a few of the common concerns.  (I’m copying the BME faculty on this message, so they can see what advice I’m giving students.)

Bioengineering, bioinformatics, MCD bio, and other departments all have different expectations or requirements for their capstone projects (which can include senior theses).  I can’t talk for any programs except bioinformatics and bioengineering.


The bioinformatics capstone is generally satisfied by the project-based grad courses that are required, but some students (20%?) also do a one-quarter or more research or development project as a senior thesis.  These theses, since they are for short projects and not an essential part of the capstone are generally fairly informal, and only 20–40 pages long.  Students planning to go on to grad school are often well advised to do research projects, and the senior thesis is one mechanism for doing that.

Because bioinformatics theses are informal and not very common, most of this message will be about bioengineering theses.  Bioinformatics students may want to look through this message for ideas about how to join labs and find projects to do, but the main audience is bioengineering students.

Bioengineering senior theses are longer and more formal than the bioinformatics ones.  The research projects consist of at least 3 quarters of BME 195 plus BME 123T in Winter quarter (so 17 units, rather than 5 units for a bioinformatics thesis).  Partly this is because wet-lab work is much slower than computer work—turnaround time for an experiment may be days or weeks, rather than minutes or hours.

thesis or group project?

Bioengineering students have the option of doing a group project for a capstone (BME 123A/B) or a senior thesis.  Those planning to go on to grad school should probably choose the thesis option, as it is better preparation for grad school.  Those planning to go into industry may be better off with the group project, though a senior thesis can also be good preparation for industry work.

If you have an idea for something you want to design and build, and can interest other students in working with you, forming a team project may be the best way to go, as faculty generally are more interested in getting help with their many research projects than with close supervision of a student-initiated project.  The BME 123AB and CMPE/EE 129ABC courses are a good umbrella for student-initiated group projects.
finding a lab and a project
No one is going to hand you an assignment and say “do this as a senior thesis!”—you have to find the project yourself.  But we don’t expect novice researchers to come up with great ideas alone (some students do come up with great ideas, of course), and so there is help in finding projects.  Generally students find projects by working with grad students, postdocs, faculty, and other researchers in a lab, and chipping off part of a bigger project that the lab is working on.  It is possible to come up with your own original project and convince a faculty member to supervise it, but that is more commonly done as group projects than individual theses, because most interesting projects are simply too big for one person to do in one year.

For the usual method to work, you need to be in a lab before you start your senior thesis.  Generally, that means finding a lab and working in it your junior year.  Bioengineering students work in labs all over campus—almost any department in the School of Engineering or the Physical and Biological Sciences could have a bioengineering project (and there are some in Social Sciences as well).

So first you need to find out what research on campus is happening and what interests you—that should start freshman year. One good way to find out what is happening in research is to attend research seminars—every department has one, generally weekly.  These are free public seminars, which you can attend without being a member of the department, signing up for a class, or anything else formal. Many of them are also listed as courses on the class schedule, so that rooms can be assigned and grad students can get credit for regular attendance (you can sign up too, if that will help you attend regularly, but make sure that you do attend regularly if you sign up—failing a no-work class for failure to show up sends a really strong message to faculty and future employers).  I particularly recommend BME 280B, the BME department seminar,  in fall quarter, since it is dedicated to showing new grad students the range of research projects available for their rotations. (Other quarters usually have different themes and other departments have different ways of organizing their seminar schedules.)

Don’t limit yourself to BME, though, as the department is too small to have enough undergrad lab positions for all the bioengineering students—bioengineering students have also worked with faculty from MCD bio, Microbiology and Environmental Toxicology, Electrical Engineering, Computer Engineering, and probably several other departments.  Some students have even taken summer research positions elsewhere and expanded those projects into year-long senior theses.

Once you have identified some research teams that look like they would be fun to join, do some homework: read the papers coming out of the group, look at their posters on the walls, talk to students who work in the lab. Once you have a fair idea what questions they are addressing and what techniques they are applying, send email to the head of the lab (often referred to as the “PI”, which is jargon for “Principal Investigator” on grant applications).  Don’t ask immediately for a senior thesis, but introduce yourself and ask if you can sit in on lab group meetings.

You may need to check out several labs simultaneously your junior year, which can take a fair amount of time in a year when you have a fairly heavy course load.

After you have been attending for a while, you might see a project that no one in the lab has time to do (there are always more ideas than time to follow up on them in a good research group).  If the lab group still seems interesting after several meetings, arrange a meeting with the PI to try to outline a possible project for you to work on.  Generally this will be a fairly small project that could grow into a senior thesis, as the PI will not want to commit the resources for a full-year project until you have proven that you are competent and reliable.

switching from finding a lab to senior thesis

Once you have  project identified and a faculty member willing to sponsor the project, you need to write up a 1–2-page proposal outlining the project and submit it to the undergrad director (that’s me).  I have not yet denied any senior thesis proposal, but the exercise of getting down in writing what you plan to do is a very important one, particularly for communicating with your PI about the scope of the project, so I’m not going to treat these as unimportant paperwork.

If the PI has not previously supervised a bioengineering senior thesis, I want to talk with them (at least by e-mail) so that they have a clear understanding of our expectations for a senior thesis (which may be quite different from the expectations in their own department—note the huge difference between a bioinformatics and a bioengineering senior thesis, even within the BME department).

The proposal should be submitted the quarter before the 3 quarters of BME 195, which generally means in the spring or summer for projects that run FWS.

We are planning to create a 2-unit “pre-capstone” course this spring to aid students in putting together group projects and senior thesis proposals.  The course is optional, but is likely to be very useful in crystallizing somewhat vague ideas into productive capstone projects and forming working groups.
what is a bioengineering senior thesis?

A bioengineering senior thesis is modeled after a PhD thesis.  It is obviously smaller (a one-year project, not a 3–7-year project), and a senior thesis does not have to be “novel work” in the sense that a PhD thesis does.  You can do an implementation of someone else’s idea for a senior thesis, but there should be substantial engineering or scientific thought on your part—you should not be merely “hands in the lab”.

A bioengineering thesis can be either a scientific one or an engineering one.  The details of what you do in the lab are similar—the difference is mainly in the goal.  A scientific thesis tries to answer a question about the real world: “what does this protein do? what is the evolutionary history of this virus?”, while an engineering thesis has a design goal “how can I move DNA slowly through a nanopore in 3M KCl? How can a get a halophilic microorganism to produce substantial quantities of butanol?”  You may end up using the same lab techniques for either sort of thesis, and you can often spin the same project as either a science or an engineering project (a lot of “science” is really engineering new lab methods, and a lot of “engineering” requires discovering new science).

Since the bioengineering major is an engineering major, I try to help students view their projects as engineering projects, especially when they are working with a PI who sees them as science projects, but there is no requirement that a bioengineering thesis must be one or the other—either is acceptable.
format of a thesis

You must write up what you do in the format of a thesis: start with a brief statement of the design goal or research question, give a detailed background on what other people have done in the past and why the problem you are tackling is important, then give a detailed description of all the design or experiments you do, including the ones that fail (and how you debugged the failures).    You do need to distinguish clearly what you do from what other people on the project do—a thesis should be written with “I” not “we” (which is different from multi-author journal papers), because the purpose of a thesis is to establish your individual research abilities.  Avoid using passive voice for the same reason—we want to know what you did, not just what was done.  When you use passive voice in a thesis, you are denying that you did it, but failing to tell us who did.

You should be writing a draft of your thesis every quarter of BME 195 and submitting it to the PI for feedback on both the content and the writing.  The first quarter should result in a draft that has a clear statement of the research question or engineering design goals, a thorough literature survey explaining what other people have done and why the question or goal you are tackling is interesting and important, and a research or development plan for how you will answer the question or achieve the design goals.  Each subsequent quarter will result in editing and rewriting big chunks of the thesis, and replacing the research plan with the research results.

The audience for your thesis is not your PI, nor even other members of your lab team.  It is other bioengineering students who might want to join the team—so you can assume that your audience has a basic knowledge of biology and engineering, but not of the specifics of your lab team’s approach.  You need to define jargon the first time you use it, and you need to give a brief intro to any techniques that you use that aren’t covered in the required courses for bioengineering students.

A thesis is not a lab notebook or a lab protocol handbook (though you may wish to give detailed protocols in an appendix to the thesis).  We are interested in the engineering thought, not how many microliters of this or that you mixed for how long—unless your engineering is optimizing the protocol, in which case we need to know why you increased or decreased pH, temperature, salinity, or whatever else you were manipulating to do your optimization.

A thesis is not a journal article.  Journal articles are very limited in space, so are carefully trimmed and edited to remove any dead ends or interesting side trips that don’t appear to contribute to the final result. A thesis should include discussion of the entire project, including the side trips and dead ends.  We want to see how you solved problems, not just the final solution, which is all the journal article usually has room for.

In BME 123T winter quarter (generally in the middle of the thesis research), we will go through several drafts of your thesis, with detailed feedback on the writing (and somewhat less on the content than the PIs are expected to give).  You should be starting Winter quarter with a complete first draft (some parts will still be plans rather than results, of course), and coming out of BME 123T with an almost complete final draft, so the spring quarter can be dedicated to finishing the research, with only a few new results to be written up.

presentation requirements

The new curriculum requires a senior portfolio containing at least two projects, one of which is your capstone project.  (The other project is generally a small one from one of your required courses.)  The portfolio also requires PDFs of three different presentation modes: a final paper, slides for an oral presentation, and a poster.  You need to make sure that you have examples of all three formats for your senior portfolio—if you are missing one at the beginning of your senior year, find a way to create it during the year.

Everyone should be producing a poster for their capstone for the undergraduate symposium in the spring (though posters produced for other venues can be included in the senior portfolio instead).  The senior thesis requires a final paper and the group projects generally require an oral presentation.  BME123T is expected to concentrate mainly on the written report format, but if students need poster or oral presentation opportunities, the course can be used for those as well.

The BME department has agreed to pay for undergrad posters printed at BELS for senior projects or for conferences for bioengineering and bioinformatics students, but NOT RUSH FEES.  If you miss the deadlines for normal charges, then the rush fees come out of your pocket (unless you can sweet-talk your PI into covering them).

2013 May 19

On labs moving from UC to private colleges

Filed under: Uncategorized — gasstationwithoutpumps @ 22:30
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Chris Newfield, starts his blog post UCLA Loses LONI: Why Budget Silence Is Bad for Science ~ Remaking the University with

There’s been much local coverage of two principal investigators switching from UCLA to USC, and taking with them an estimated 85 people from UCLA’s Laboratory of Neuro Imaging (LONI). The Los Angeles Times has run two stories about it, one of which received over 120 reader comments, and the story was Larry Mantle’s lead on his Airtalk show at KPCC, where he had one of the two departing faculty members as his guest.

But beyond a big win for the Trojans over the Bruins, why should the public care?

He goes on with an analysis of the importance and the cost of doing science research at UC, pointing out that the particular PIs lured away were very highly compensated:

I don’t know LONI’s equipment and infrastructure issues at UCLA, but the only publicized financial information was of the leaders’ salaries: over $1 million / year for Prof. Toga, over $420,000 for Prof. Thompson. A good number of highly qualified people will line up for jobs like these.

I had much the same reaction—those are not public university salaries.  A dozen top-notch assistant and associate professors could be hired for what those two were paid.  USC is welcome to sink their money into hiring big names—perhaps they could hire away all the athletic coaches from UCB and UCLA as well (please).

Chris got a lot of flak in the comments for his simile about the cost of doing research:

Public universities can’t fully support their grants because extramural funding doesn’t cover the full cost of research.  Labs burn money like a jet burns fuel, which is what they are supposed to do.  LONI spent $12 million a year, as a case in point. 

$12 million dollars for 85 people is only $141k per person.  Given the huge salaries of the PIs (not to mention the costs of their benefits), the expenditure per person for the other 83 was under $125k, and salaries were probably less than half that (given the necessary costs for reagents, equipment, travel, publication charges, benefits, …).  So most of the lab was making only modest salaries—only the PIs were raking in the dough.

Chris ended with 4 conclusions:

  1. UCLA’s core problem is a funding shortage, not surplus bureaucracy. (UCLA is the wealthiest UC campus, so things only get worse from there). 
  2. Public universities need to tell the truth about research funding.  This will include the facts that science loses money, that some portion of undergraduate tuition funds offset research costs, and that most funding doesn’t “produce” anything in the near-term, except findings [for] more research along with a great deal of useful failure.
  3. Public universities need to explain why research like LONI’s should be to some large extent at public universities.  Why does it matter to the science, to the public impact, to the education of the next generation of scientists? Perhaps there is more openness and accountability at publics, and therefore more innovation. Perhaps scientists at public universities have a better feel for public needs and do more useful research.  Perhaps public universities uniquely have the necessary scale to train the thousands and millions of researchers in all fields to solve our ever-mounting problems.  We now need a new theory of public universities, before things get even worse.
  4. Universities both private and public need to open up  discussion of spending priorities to their academic communities.  Given rising costs and shrinking revenues, choices have to be made. They  need to involve the faculty, from all disciplines, and students of all levels.  This is as true of USC as of UCLA, which has a poor record of consultation and can only buy a limited number of LONI-type labs with (in part) student tuition and non-STEM cross-subsidies.  Privates can now raise tuition only so much. Academic choices need to come from a bottom-up debate of a kind that higher ed has never had.

There was an excellent discussion in the comments to his post, mainly pushback on point 2, as STEM faculty see their overhead being spent on everything in the university except the proper indirect expenses that it is supposed to go for, while Chris looked at the overall expenditure on support for science research and the income from indirect costs.  I think that a lot of the discrepancy comes from the cost of new buildings for science labs, which are very, very expensive, but cannot be charged to grants.

I’m in agreement with Chris that UC has done a very poor job of making a good case for research in the public universities, talking about it mainly as a revenue stream or in PR terms as enhancing the image of the university.

In one of Chris’s comments, he restates his main point as a desire for greater budget transparency:

So my suggestion as always is that faculty across the disciplines stop being cynical about “byzantine accounting” and push for full data on funding flows—universities can’t even start the negotiations for ICR rates without this accounting to show federal agencies—let the chips fall where they may, and then have an involved discussion based on actual budgetary facts about what to do. My position is always that I do not want cuts to STEM research. I want research to be fully funded. The patchwork we have doesn’t work any more—for any field. Things will continue to deteriorate unless we can drop our longstanding mental habits get clarity on how our own institutions work .

I think that greater clarity in how funds flow around the university would be helpful—particularly to those of us at the underfunded campuses (UCB and UCL have long gotten far more than a fair share of state funds and tuition dollars, and even the “rebenching” now in progress has been carefully designed to perpetuate the inequity).  If the research grants are not paying what the research costs the University, then indirect costs need to be raised, or the state needs to provide explicit support for research to cover the costs, or the University has to make a much, much better case that undergrads benefit from the research and so their tuition should be used to cover the shortfall.

I think that the case for undergrad benefit is quite different on different campuses and even in different majors.

For example, in the bioengineering major at UCSC, all the undergrads do research, either individually with faculty, postdocs, and grad students, or as part of a group project supervised by faculty.  They use equipment and labs funded by research grants and get a lot of high-contact instruction in these projects that could not be duplicated without the money brought in from federal grants, grants from non-profits, and even industrial research contracts.  Some of the undergrad students in the bioengineering major are doing exceptional research, and all are being very well prepared for grad school.  I have no trouble asserting that these students are benefiting substantially from the active research programs in biomolecular engineering and molecular biology.

On the other hand, I’ve recently been visiting colleges to find a good place for my son to apply in computer science (see College tours around LA and UC Berkeley college tour), and neither UCB nor UCLA had much involvement of undergrads in computer science research. I’d have a hard time telling a student whose smallest class in their major had over 50 students and most upper division courses had 200, that research opportunities for 5–10% of the undergrad students were a good deal for them. (To be fair, this may be more discipline-specific than campus-specific, as the computer science department at UCSC also seems to have less involvement of undergrads in research than the other engineering departments.)

It is not clear to me whether student tuition is supporting the research mission or research grants are supporting student instruction.  I’ve seen arguments for both, and I don’t really believe any of the arguments are really solidly based on facts.  The UC budget is such a tangled web of inconsistencies that people can read anything into it that they want.

Although UC has certainly failed on budget transparency, I think that the bigger discussion that has been missing is Chris’s point 3, explaining why research is an essential part of the mission of some public universities.  Obviously it is not essential for all (neither the community college system nor the California State University system have research as a major part of their missions), but UC administration and faculty have never made a clear case to the public of the need for research in a public university.  I think that it is time to do so, but I don’t know that I can put together a clear case for it—certainly not to the point where I could say how much of student tuition should be going to support the research mission.

2012 January 15

Individual work in collaborations

Filed under: Uncategorized — gasstationwithoutpumps @ 12:09
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I have protested in this blog before about the excessive use of inappropriate group work in schools, though recognizing that there are projects that are big enough or varied enough that groups are the appropriate way to tackle them.

A much more eloquent article on the subject by Susan Cain was just published in the NY Times: The Rise of the New Groupthink.

There are nice sound bites like

But decades of research show that individuals almost always perform better than groups in both quality and quantity, and group performance gets worse as group size increases.

She does suggest that on-line brainstorming may work better than in-person brainstorming, quoting Proust’s description of reading as a “miracle of communication in the midst of solitude”.  Her prescription for effective teamwork seems reasonable to me:

To harness the energy that fuels both these drives, we need to move beyond the New Groupthink and embrace a more nuanced approach to creativity and learning. Our offices should encourage casual, cafe-style interactions, but allow people to disappear into personalized, private spaces when they want to be alone. Our schools should teach children to work with others, but also to work on their own for sustained periods of time. And we must recognize that introverts like Steve Wozniak need extra quiet and privacy to do their best work.

I certainly have found that my best collaborative work has come out of fairly incidental contacts (meeting someone from another department in a hallway, chatting after a research seminar, talking with a student in someone else’s research group), followed by days or weeks of intensive work on the problem.

My sabbatical this year has been going through fertile and dead periods.  The dead periods have been times when I was not getting any contact with students and colleagues, and was not getting anything done.  The fertile periods were intense bursts of activity by myself after a chance contact with someone sparked an interest in a particular problem.

Most recently, I’ve been working on putting together a bioinformatics protocol that will let us reconstruct the cagY genes from hundreds of strains of Helicobacter pylori using PacBio sequencing.  Most of the sequencing technologies are not suitable for this gene, as it has long blocks of many repeats that vary from strain to strain.  Because the tandem replication is very recent (divergence between the strains may be only a few generations earlier) and there is selective pressure to maintain the open reading frame, the different repeats are often identical for long stretches, making short-read data nearly impossible to assemble. Even Sanger sequencing to confirm the gene assembly is difficult, as it is hard to find unique primer locations.

I started this project as a result of a short discussion with a couple of H. pylori researchers, but I spent weeks writing programs and Makefiles, testing them, twiddling parameters to see if they were robust, and so on.  I could not have done the work without the collaboration (I needed someone who had a difficult, interesting problem and the data to work on), but I could not have done the work if someone had kept interrupting me or making suggestions either.  The project would probably have died halfway through if I had had to do it with my usual teaching load, as I was spending 12–16 hours a day on it for weeks.

I need to alternate between working alone and contact with others. Sometimes talking through a problem with someone who understands and can ask good questions helps me clarify my thinking, after which I need hours or days to work out the details, after which I want to share again.

2011 December 2

I made it through National Blog Posting Month again

Filed under: Uncategorized — gasstationwithoutpumps @ 17:19
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At the beginning of November, I committed to writing a blog post a day for National Blog Posting Month (NaBloPoMo), an exercise that has gotten many people to post more to blogs.  Whether getting more people to blog is a good thing or not depends on how much you value blogs—I find that a lot of my time is now wasted reading many blogs, though I occasionally pick up a useful or interesting nugget of information.

I managed once again to write a post a day, mainly by working in bursts, queuing up four or five posts to trickle out one a day. I still have over 100 draft posts to write, as new prompts for posts arrive at an average rate of about one a day.  Some of them will get stale before I get around to writing anything on them, and some (like my unwritten research papers) will sit around forever reproaching me for not tackling them.  My readership for November 2011 was not bad (5800 views), but not my record monthly readership.

As I wrote last year in Writer’s Block, reducing my barriers to getting stuff written was part of my reason for starting a blog, and last November when I joined NaBloPoMo, I said “If I make it through November at a post a day, I can try to dedicate December to getting out some of my research papers that are long overdue for publication.” That didn’t work last year, but let’s see if I can do better this year.

A lot of my more recent work is waiting for collaborators to finish wet-lab validation (the banana slug Ariolimax dolichophallus mitochondrial genome, the Vibrio cholerae genome, the Helicobacter pylori genome), while slightly older stuff is waiting for collaborators to have time to do some of the writing (the Pyrobaculum oguniense genome).  The really ancient stuff is mostly protein-structure prediction stuff (the scoring function for disulfides, scoring hydrogen bonds without explicit hydrogens, conformation change operators in undertaker, …) and I really have a hard time getting up any enthusiasm for it.  The disulfide paper has been written for 2 years, and I still haven’t submitted it—perhaps I should remove the courtesy co-author who added some delays and submit it to some minor journal.

I did this month get some PCR data on the Vibrio cholerae genome, confirming some of the things I was worried about in the first assembly.  I redid the assembly using a slightly different method, and got a dozen or so major differences, so I’m having to request some more PCR to see which of the assembly techniques is more accurate.  Both were using the same 454 data (plus some Sanger sequencing of PCR reactions for the second assembly, but they made no difference).  The big difference was in whether I did a mapping assembly (using a previously sequenced strain of Vibrio cholerae), or did a de novo assembly and ordered and oriented the contigs by mapping to the previous assembly.  With the mapping assembly, I had fewer differences from the reference genome, but I don’t know whether this is because the de novo assembly failed to assemble some parts or if the mapping assembly copied parts of the reference for which there was really insufficient data.  A lot of the changes were in repeat regions (like the ribosomal operon) that could easily have degraded in some copies, so there is no way that I can tell which assembly is right, other than by having PCR reactions done to look at the length or the sequence of DNA between distinctive primers. It feels good to have gotten some productive work done, even if not written up.

Other productive work this quarter includes the improved velocity and acceleration extraction in Tracker (which I probably won’t write up other than in my blog, unless someone can recommend a journal for which it is appropriate—and not an author-pays journal).

I have gotten the ghmm package working on my laptop again (it had been broken by the installation of Vpython—Vpython insists on 32-bit Python, but ghmm compiles only for 64-bit Python on a 64-bit architecture), so I can get back to work on the HMM analysis of nanopore current data again.  If I get something working there, I can probably get a co-authored paper out with the nanopore people who generate the data.

2011 October 4

Sabbatical plans 2

Filed under: Uncategorized — gasstationwithoutpumps @ 20:32
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As I reported in Sabbatical plans in June, I’m on sabbatical now, for the first time in 7 years.  I’m not planning to go anywhere, except for short visits.  I’ve done one 1-week trip to Italy, to give invited talks in Ravenna and Bologna, and I’ll be going to Washington, DC later this month for an NSF panel to review proposals.

I haven’t had quite as much time for research as I had expected, since I’ve been on several thesis committees.  (I have an advancement to candidacy exam and a dissertation defense to go to this week—both with long, detailed papers to mark up.)

I still plan to use the year to refocus and restart my research and to think long-term about how I will work for the next decade. Will I concentrate more on teaching? Will I do research primarily as a collaborator (not writing grants)? Will I be doing a lot of grant writing to try to start a new research group?

Here were some of my options described in June:

  • Write up and submit 2–10 papers on old research that never got written up (didn’t do any of these over the summer):
    • N-CA-C bond angle scoring
    • H-bond scoring without explicit hydrogens
    • Disulfide bond scoring
    • Conformation-change operators for tweaking proteins
    • Genome of Pyrobaculum oguniense
    • Virus that lives in Pyrobaculum oguniense and its integrase
    • Genome of Helicobacter pylori (the lab strain used locally)
    • Use of PacBio long reads to resolve a long, important repeat in Helicobacter pylori
      I did some work on this over the summer and am waiting for wet-lab verification
    • Genome of Vibrio cholerae (the lab strain used locally)
    • Assembly methods for high-quality prokaryote assembly from next-gen data using not-quite-clonal populations
    • Mitochondrial genome for Ariolimax dolichophallus
      I did some work on this over the summer and am waiting for wet-lab verification
  • Decide what field to go into next.  Currently I’m considering two main choices: computational protein design and genome assembly. I’ve done nothing on protein design over the summer, but I did do some detail work on the repeat regions in Helicobacter pylori‘s cagY gene and in the Ariolimax dolichophallus mitochondrion.
  • Take courses (I’ve never had O. chem or enzyme mechanics, which could be useful if I go into protein design)  I didn’t feel like taking courses this quarter, but I taught myself printed-circuit board design over the summer (not cutting-edge design, but simple 2-layer design, suitable for low-cost hobbyist boards). I’ve even been thinking of teaching hobbyist-level PC board design through Makers’ Factory.
  • Write programs. This is the most fun thing on my list, but I have to decide which programs to write.  So far I’m committed to collaborations involving a new optical mapping technique (nothing done on that at all) and nanopore data analysis (did some simple statistics for a paper, but haven’t made any progress on the HMM program since June). I’d really like to start something that could be a killer app in genome assembly. I’ve written a lot of small Python programs for utility application in genome assembly, but each project has needed a different set of tools: I’ve not come up with anything that was worth the effort of re-writing in a more efficient language.
  • Write grant proposals. This is the one I dread most—I don’t handle rejection well, and I’ve had my last 10 or so grant proposals rejected. I’m also beginning to see the grant-writing game as mainly a way for the government to slow down the progress of research, so that things don’t change too fast for the bureaucrats.  I’m wondering if the university and I would be better off if I didn’t waste time in futile chasing after grants, and spent my time on teaching and research instead.  The downside is that I’d not be able to support students, since there is now almost no provision for supporting engineering students outside of research grants.  Some of my best work lately has been collaborations with other research groups, though, so maybe I should give up on controlling the money flow, and just work with people who have money.
  • Write a book.  I’m not a particularly fast writer, so it would take a full year.  I was thinking of a project I started back in 1981 and have played with as a hobbyist for a few months once a decade since.  The book would be written for hobbyists, but contain enough tutorial material that it could be used to really learn the subject.  I started doing bits of this in another blog, but I got sidetracked into doing printed-circuit board design instead of the stuff that would be appropriate for the book project. It seems unlikely that I’ll do a book this year.
  • Develop new courses. I don’t have any ideas for new courses, though it might be worthwhile to redesign the banana-slug genomics into an upper-division undergrad class—we need undergrad classes more than we need grad classes. I’d have to expand the content to include more prokaryote assembly and maybe even some metagenomics.  Perhaps I should also see if the instructor working on the applied electronics class for bioengineering students wants any help from me—he’s a good person to work with.
  • Work on K–12 education.
    • I’m on a task force that is trying to get bioinformatics into AP bio—I’m still thinking I could work with a local high school teacher to develop and test some lessons that use bioinformatics to teach crucial content in the AP course, but I’ve neither identified a bioinformatics lab to push nor contacted the teacher who might be interested.
    • I’m still coaching a high school robotics team, though now it is a city-wide team, with students from two different schools.  I’ve been putting a lot more time into this than I had expected (the printed-circuit boards I designed will be used by the robotics club).
    • I am learning calculus-based physics along with my son and another high-school student. (See physics posts.)

My prediction in June that “I’ll end up dinking around with several of the ideas and being dissatisfied with the amount I get done on any one of them” seems to be holding true so far.  Perhaps after I’ve cleared the advancement to candidacy and dissertation reading and the reviewed the 100s of pages of NSF proposals, I may be able to focus on something and have a productive sabbatical.

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