Arjun Rao
For catalog copy and pre-requisites, see the main page for BME200.
lecture and discussion section (REQUIRED): PSB 305 Thurs 2–3:45
Do not take BME 200 for a letter grade!
The lectures and discussions will cover topics specific to bioinformatics, including such things as lab safety and cultural differences between the academic cultures of biology and computer science, as well as more general graduate student stuff, such as how to write a research paper, avoiding sexual harassment, fellowships, library usage, LaTeX, ...
All new grad students should plan on taking 280B this quarter, since it will be a series of introductory lectures by faculty who can accept grad students into their labs for lab rotation projects.
There will be a small number of written assignments for this class: a LaTeX exercise, a library/BibTeX exercise, writing a fellowship or grant proposal, and a web page exercise.
The course is graded strictly on the Satisfactory/Unsatisfactory scale. Do not register for a letter grade.
Homework assignment: LaTeX assignment Due 10 Oct 2013. Reproduce the example in latex-assign.pdf using LaTeX.
Homework assignment: fellowship application Due Fri 18 Oct 2013 (joint with BME 205).
Homework assignment: LaTeX/BibTeX assignment Due 21 Nov 2013.
Homework assignment: Web page assignment Due 5 Dec 2013 (last day of classes)
Required:
Anyone caught cheating in the class will be punished severely—most likely failed in the class and possibly thrown out of grad school. Cheating includes any attempt to claim someone else's work as your own. Plagiarism in any form (including close paraphrasing) will be considered cheating. Use of any source without proper citation will be considered cheating.
Collaboration without explicit written acknowledgment will be considered cheating. Collaboration on some assignments with explicit written acknowledgment is encouraged—guidelines for the extent of reasonable collaboration will be given in class.
Who is in the class this year. I'm trying to learn the names of this year's students. I'm hoping to have them all straight within 10 weeks. That doesn't sound very challenging with so few students, but I have real trouble with names.
Note: FERPA prohibits the dissemination of academic records without permission, and UCSC has taken the particularly paranoid view that any mention of a student could be considered an academic record. So pictures and names can't be posted here without student permission. Other faculty and grad students use these pictures to help get to know who the new students are (with our tiny department spread over 6 different floors in 4 buildings, a physical bulletin board of students wouldn't help much), so I encourage students to allow their names and pictures to be posted.
The pictures below have links to larger images.
Note: list should be updated throughout the quarter to reflect what really happens.
Discussed textbooks and assignments, grad requirements, did some group advising on courses.
If you like this blog, you might want to check out others on this list of blogs by female scientists: http://www.guardian.co.uk/science/the-lay-scientist/2010/sep/16/women-science-blogging , though it might be a bit UK-centric.
Staff members' access to confidential student information is accompanied by a responsibility for understanding and following the policy on the privacy of student records. For information, please see the Privacy of Student Records page on the Registrar's Office web site. http://registrar.ucsc.edu/records/privacy/index.html One of the links in the Resources section of that page is to the UCSC Policy on the Privacy of Student Records quick guide. http://registrar.ucsc.edu/records/privacy/disclosure_qr.pdf In addition to the training resources also available, you may wish to review the Essential Information for Faculty, Teaching Assistants, and Readers, at the FERPA for faculty link in the Resources section. http://registrar.ucsc.edu/records/privacy/FERPA-for-faculty.pdf
TAships and union activity
Instructor Checklist for TAs. All TAs need to consult with the instructor they are working for, and discuss the TA responsibilities at the beginning of the quarter. Once both parties agree on what the TA needs to do, they need to sign the checklist. This is a requirement of the job. The checklist forms can be found on http://ga.soe.ucsc.edu/current/forms, and you can compare these with the union's information at http://www.uaw2865.org/member-resources/. They have a generic checklist on their page http://www.uaw2865.org/member-resources/ase-checklist/
Running discussion sections, workload, TA union and strikes. Brief mention of AAUP and their publication Academe, which is available on-line as http://www.aaup.org/AAUP/pubsres/academe/
Handout on Center for Teaching and Learning and their services: TA Starter Package
informal discussion of TA union and how to fix problems before
triggering the union grievance process.
Contacting your union steward:
UAW Local 2865
310 Locust St., Suite B / Mailbox 2
Santa Cruz, CA 95060
Fax (831) 423-3606
santacruz@uaw2865.org
http://www.uaw2865.org/home/home.php
Note: TAs are not allowed to have office hours in shared grad-student space. TA office hours are to be scheduled in Baskin Engineering 312 C and D by Tracie Tucker. See http://ga.soe.ucsc.edu/ta/office-hours for more information.
There have been grad computing labs in Baskin 314A and 316, for which you would need keys different from the BME grad key that opens the labs in Physical Sciences Building—few BME students have opted to use the Baskin computers.
Discussion of advancement to candidacy and thesis committees.
Homework assignment: LaTeX assignmentThe purpose of this assignment is to develop some preliminary facility with LaTeX, particularly with math equations and tables. You are to try to duplicate (approximately) the 2-page paper in latex-assign.pdf
Went over some examples of a basic LaTeX paper in example.tex and the corresponding output example.pdf. You can use "make" to do the repeated calls to latex with the Makefile
I strongly recommend using LaTeX for thesis proposals and theses. There is a style file available (which I have not checked myself, but which should be a good starting point at least) in http://www.soe.ucsc.edu/~you/notes/ucthesis-ucsc/
There is a cool tool for guessing the LaTeX code for hand-drawn symbols at http://detexify.kirelabs.org/classify.html Personally, I find it faster to scan a list of symbols (particularly since drawing with a touch pad on a laptop is tough), but others may find this drawing approach useful. The comprehensive list at http://www.tex.ac.uk/tex-archive/info/symbols/comprehensive/symbols-a4.pdf is a useful one.
Covered preparing a document with LaTeX. Using a Makefile and gnumake to run LaTeX, BibTeX, dvips, and distill. Explained difference between distill and ps2pdf, but did not talk about how to set up ssh to do passphraseless ssh to apache or sundance to run distill.
Setting up your PRINTER environment variable correctly: see instructions at http://support.soe.ucsc.edu/printing
On my Mac, I use the small distribution BasicTex on my Mac, because it is quick to download, takes up little disk space (only 86Mbytes), and has everything I use. Some people prefer a GUI interface like TeXWorks.
Turn in both the .tex source and the printed output at the beginning of class.
Classroom accommodations for disabilities
The Dean for Undergraduate Education (William Ladusaw) recommends
incorporating the following paragraph into all syllabi:
"If you qualify for classroom accommodations because of a disability,
please submit your Accommodation Authorization from the Disability
Resource Center (DRC) to me during my office hours in a timely manner,
preferably within the first two weeks of the quarter. Contact DRC at
459-2089 (voice), 459-4807 (TTY)."
The DRC has provided an updated and comprehensive faculty resource page at: http://drc.ucsc.edu/fac-staff/faculty/index.html and they call particular attention to exam accommodation: http://drc.ucsc.edu/fac-staff/faculty/faculty-exam-sheet.html They also have a link to requirements of the Americans with Disabilities Act (ADA) for grad students as employees, students, teachers, providers of public service, and web developers.
Last year, the DRC sent out a message with a lot of links in it that I put in last year's web page for this course. They have since scrambled their web site so that none of the links are good any more. Note: this is standard practice at UCSC—there is not much point in keeping bookmarks for long, as the web masters on campus believe in scrambling the web pages frequently. Learn some keywords and do Google searches, and hope that the frequent web scrambling doesn't cause the information you need to disappear completely.
(Image cleaned up from
http://chzoddlyspecific.files.wordpress.com/2010/07/ecd7fef9-6190-4efe-b70d-84608866d526.jpg)
\begin{eqnarray}
\hbox to 5pt{$E(c^2) =$ \hskip 0pt minus 1fill} & & \nonumber\\
&=& \lambda^{-2} \int_{-\infty}^{\infty} {y^2\over(1+e^{y})(1+e^{-y})} dy \\
The main missed point on LaTeX was that several people did not use the \label and \ref commands for creating cross-references.
/projects/compbio/papers/tex/citations.bibPut
setenv BIBINPUTS .:/projects/compbio/papers/tex::in your .cshrc file and say \bibliography{full-journals,my,citations,crossrefs} to include both your file my.bib and /projects/compbio/papers/tex/citations.bib in your search for bibliography entries. (See the notes at the beginning of citations.bib for more info, including fancy tools like pmid2bib and update-journals.)
Writing proposals (thesis proposals, funding applications, ...) (Covered in BME 205.)
Over 20 examples of thesis proposals that passed can be found on the BSoE file servers at /projects/compbio/papers/thesis-proposals/
Funding sources.
lab safety may be a familiar topic to those who came from wet-lab backgrounds, but those who are coming in from the computational side really need to learn this stuff! UC has also gotten much more strict about lab safety in the past couple of years, so sloppy lab safety practices you may have learned earlier will not be tolerated.
Check out the Office Ergonomics page for information about ergonomics. Avoid the wrist and back problems that plague so many computer people! There is a computer workstation self-assessment at http://ehs.ucsc.edu/programs/ergo/#OES
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