UBC Reading Group Mailing lists

https://www.cs.ubc.ca/~csgsa/pmwiki.php/Main/ReadingGroupListing

Professor Proverbs

http://www.phdcomics.com/comics.php?f=1591

Mental health: Under a cloud

http://www.nature.com/nature/journal/v490/n7419/full/nj7419-299a.html?WT.ec_id=NATURE-2012-10-11

Depression is rife among graduate students and postdocs. Universities are working to get them the help they need.

She developed a crippling fear of presenting her research. “Doing a PhD is such a personal thing, one that you've invested so much time in, that any criticism can feel like a direct reflection of yourself,” says Lauren.

But she did something that many postgraduates do not: she got help. With counselling and medication, Lauren — a pseudonym that she uses on a blog detailing her experience (see go.nature.com/4ta9fo) — is entering the final year of her PhD. Hers is one of more than 50 stories highlighted on the website Students Against Depression, funded by the Charlie Waller Memorial Trust in Thatcham, UK. “The website aims to raise awareness that depression isn't a personal failing or weakness; it's a serious condition that requires treatment,” says psychologist Denise Meyer, the website's project manager.

“Getting help,” she says, “is a sign of strength, not weakness.”

Advice for Beginning Your PhD Career

http://web.bii.a-star.edu.sg/~stanley/Advice%20for%20Beginning%20Your%20PhD%20Career.pdf

by Idris Hsi

"One is reminded of Harry Lime's famous quip in the movie 'The Third Man' that 30 years of noisy, violent churning under the Borgias in Italy produced Michelangelo, Leonardo da Vinci and the Renaissance, while 500 years of peace, quiet and harmony in Switzerland produced the cuckoo clock.

'A monolithic framework does not create a critical mind,' remarked the religious philosopher David Hartman. 'Where there is only one self-evident truth, nothing ever gets challenged and no sparks of creativity ever get generated. The strength of America has always been its ability to challenge its own truths by presenting alternative possibilities. That forces you to justify your own ideas, and that competition of ideas is what creates excellence.'"

(Friedman, Thomas "Cuckoo in Carolina", The New York Times,
August 28, 2002)

While both these quotes address the disadvantages of stability and monochromatic thinking at the societal level, they indirectly speak to the disadvantages of maintaining a one-sided view of research, research techniques, or a research area. Good research requires the rigor of scientific objectivity.

a) Get your ego out of the way. 

b) Learn to examine all sides equally.

c) Read outside your area.

d) Learn how to discuss other people's research in addition to your own.

Advice for potential graduate students

http://www.biology.duke.edu/johnsenlab/advice.html

First, be realistic about graduate school. Graduate school in biology is not a sure path to success.

Second, choose your advisor wisely. Consciously and unconsciously, you will imitate your advisor.  Your career will mostly take care of itself, but you can't get your youth back.

Finally, have your fun now. Five years is a long time when you are 23 years old.

Thesis defense advice

Think of your thesis examiners as your students, you're trying to teach them about your work and discuss things for future improvement.

http://www.uoguelph.ca/~gardnerw/research/defence.htm
http://custompapers.com/essays-articles/defending-thesis-dissertation/
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2008_07_25/caredit.a0800111
http://students.utsi.edu/nsbe/thesis%20defense%20guidelines.ppt
http://www.ips.um.edu.my/images/ips/doc/slides_upskill2012/Thesis_Defense.pdf
https://webspace.utexas.edu/cherwitz/www/ie/m_jalongo.html 

http://www.labspaces.net/blog/1390/Ten_tips_to_give_a_great_thesis_defense

Turning point: Rachel O'Reilly

http://www.nature.com/naturejobs/science/articles/10.1038/nj7401-149a?WT.ec_id=NATUREjobs-20120607

You spent some time working alone before collaborating with other researchers. Why?

You have to be able to develop the technology and the methods yourself first, so that you can then go on to make a contribution as a collaborator. That is probably harder for younger people. You can get approached to collaborate while you are still developing ideas and methods, and then end up unable to produce what you need for the collaboration to work. I held off for a few years to actually make sure I could say, 'Yes, we can make that; yes, we can do that'.

What has been your most difficult challenge?

Having grants and papers rejected are probably the things I've found hardest. You have to be able to accept failure. I still feel that when I am talking about my research ideas I am baring part of my soul. It is a very personal thing. I have learned to realize that a rejection may be the result of not communicating my ideas effectively, and not because I am a failure. I try to use negative criticism as constructively as possible.

Postgraduate options: Academia misses the mark

http://www.nature.com/naturejobs/science/articles/10.1038/nj7399-535a?WT.ec_id=NATUREjobs-20120607

Many faculty members still don't realize that only a tiny fraction of US postgraduates land a tenure-track academic research position, says Patrick Brandt, director of science, training and diversity at the University of North Carolina in Chapel Hill. Brandt, a former biochemist, has also initiated several career-advice programmes, including one in which former researchers talk about their non-academic careers. “We are ethically bound to provide broad-spectrum career guidance to rising biomedical scientists,” he says.

Soh says that those who are in a position to influence students are showing subtle, but encouraging, signs of a shift away from the pro-academia bias. “It's not a tidal wave,” she says. “But more questions are being asked and there is more momentum building.”

JANE - Journal / Author Name Estimator

http://www.biosemantics.org/jane/suggestions.php


Have you recently written a paper, but you're not sure to which journal you should submit it? Or maybe you want to find relevant articles to cite in your paper? Or are you an editor, and do you need to find reviewers for a particular paper? Jane can help!

Just enter the title and/or abstract of the paper in the box, and click on 'Find journals', 'Find authors' or 'Find Articles'. Jane will then compare your document to millions of documents in Medline to find the best matching journals, authors or articles.

Thesis writing figure captions and cross-references

http://office.microsoft.com/en-us/word-help/inserting-cross-references-HA001186680.aspx

References menu > Insert Caption (Cross-reference) button

Select text (or Ctrl-A for all) then F9 to update cross-references

Professional master's degree

http://www.nature.com/nbt/journal/v30/n4/full/nbt.2180.html?WT.ec_id=NATUREjobs-20120419


Many PhDs are finding out the hard way how challenging it is to obtain that first position out of the academic laboratory. The skills learned as a PhD student or postdoctoral scientist do not always translate into industry and are often not enough to impress employers. All things being equal, employers will always hire the PhD with additional business administration training.

The reality is now setting in for many PhDs that they need additional training. Professional master's degrees have a proven record of benefitting individuals trained in science, reorienting their career towards nontraditional fields. The monetary and time investment that goes into obtaining a professional master's degree, although significant, is in the end worthwhile.

Poster Genius

http://www.postergenius.com/cms/index.php

Create your best scientific postereasily, in less than 10 minuteswith PosterGenius™

ResearchGate - Facebook for research

http://www.researchgate.net

Picking advisors and committee members

http://www.experience.com/alumnus/article?channel_id=advanced_degree_development&source_page=home&article_id=article_1150430925421

http://edit911.com/2011/03/choosing-your-dissertation-committee/

http://www.articlesbase.com/writing-articles/choosing-your-dissertation-committee-4366352.html

Ten Simple Rules for Teaching Bioinformatics at the High School Level

Ten Simple Rules for Teaching Bioinformatics at the High School Level

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002243

Checklist

1. Am I energized to be enthusiastic about this class?
2. Is the classroom arranged properly for the day's activities?
3. Is my name, course title, and number on the chalkboard?
4. Do I have an ice-breaker planned?
5. Do I have a way to start leaming names?
6. Do I have a way to gather information on student backgrounds, interests, expectations for the course, questions, concerns?
7. Is the syllabus complete and clear?
8. Have I outlined how students will be evaluated?
9. Do I have announcements of needed information ready?
10. Do I have a way of gathering student feedback?
11. When the class is over; will students want to come back? Will you want to come back?

Ten Simple Rules for Getting involved in your scientific community

Ten Simple Rules for Getting involved in your scientific community

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002232

Activities such as organizing conferences and workshops, answering questions and discussing scientific ideas online, contributing to a scientific blog, or participating in open source software projects are typically thought of as outside classic research activity. Having scientists involved in those activities, however, is very important for the community to be dynamic and to promote fruitful discussions and collaborations.


encourage your colleagues to play an active role in the scientific community
want to maintain a balance with the activities directly related to your research projects
remember that you are not alone
If you know why you are doing it and if you enjoy it, you will take the time to do it, and you will do it well

Erroneous analyses of interactions in neuroscience: a problem of significance

http://www.nature.com/neuro/journal/v14/n9/full/nn.2886.html

Whatever the reasons for the error, its ubiquity and potential effect suggest that researchers and reviewers should be more aware that the difference between significant and not significant is not itself necessarily significant.

A fictive example would be “Hippocampal firing synchrony correlated with memory performance in the placebo condition (r = 0.43, P = 0.01), but not in the drug condition (r = 0.19, P = 0.21)”. When making a comparison between two correlations, researchers should directly contrast the two correlations using an appropriate statistical method.

Ten Simple Rules for Getting Help from Online Scientific Communities

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

results in research only begets for more questions

results in research only begets for more questions

Options for collaborating with LaTeX

http://tex.stackexchange.com/questions/4489/what-is-a-good-strategy-for-obtaining-comments-on-a-latex-document-from-non-latex
http://stackoverflow.com/questions/539791/tips-for-collaboratively-editing-a-latex-document
http://luca.cse.ucsc.edu/Style_guidelines_for_student_co-authors

- use latex2rtf to export it to an rtf file which can be opened in word
- export to PDF and have the PDF edited using Acrobat Pro
- add line numbers, manual e-mail of revisions

both will need some manual editing to apply changes back to latex :(

- or do everything in word first, then make the final submission in latex?