Friday, February 24, 2012

Mu-ming Poo's Letter

Mu-ming Poo is head of the Division of Neurobiology, Department of Molecular and Cell Biology at University of California, Berkeley, California, USA. He is also director of the Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China.

I cannot attest to the provenance of this, but I’ll quote anyway:

To all lab members:

Over the past several months, it has become clear to me that if there is no drastic change in the lab, Poo lab will soon cease to be a productive, first-rate lab that you chose to join in the first place. Lab progress reports over the past six months have clearly shown the lack of progress in most projects. One year ago, when we first moved to Berkeley, I expressed clearly to everyone my expectation from each one in the lab. The most important thing is what I consider to be sufficient amount of time and effort in the lab work. I mentioned that about 60 hr working time per week is what I consider the minimal time an average successful young scientist in these days has to put into the lab work. There may be a few rare lucky fellows like Florian, who had two Nature papers in his sleeve already, can enjoy life for a while and still get a job offer from Harvard. no one else in the lab has Florian\'s luxury to play around.

Thus I am imposing strict rules in the lab from now on:
  1. Every one works at least 50 hr a week in the lab (e.g., 8+ hr a day, six days a week). This is by far lower than what I am doing every day and throughout most of my career. You may be smarter or do not want to be as successful, but I am not asking you to match my time in the lab.
  2. By working, I mean real bench work. This does not include surfing on the computer and sending and receiving e-mails for non-scientific matters unrelated to your work (you can do this after work in the lab or at home), and excessive chatting on nonscientific matters. No long lunch break except special occasions. I suggest that everyone puts in at least 6 hr concentrated bench work and 2+ hr reading and other research-related activity each day. Reading papers and books should be done mostly after work. More time can be spent on reading, literature search and writing during working hours when you are ready for writing a paper.
  3. I must be informed in person by e-mail (even in my absence from the lab) when you are absent from the lab for a whole day or more. Inform me early your vacation plan. Taking more than 20 working days out of one year is the maximum to me. In fact, none of you are reporting any vacation and sick leave on your time sheet (against the university rule, although I have been signing the sheets), but you know roughly how many days you were not here.
On the whole, I understand and accept the fact that you may not fulfill the above requirements all the time, due to health reasons, occasional personal business. But if you do not like to follow the rules because it is simply a matter of choice of life style, I respect your choice but suggest you start making plans immediately and leave the lab by the end of January 31. I will do my best to help you to locate a lab to transfer or to find a job. If you do accept the conditions I describe above, I am happy to continue to provide my best support to your work, hopefully more than I have done in the past. I will review the progress of everyone in the lab by the end of June of 2002. I expect everyone to have made sufficient progress in the research so that a good paper is in sight (at least to the level of J. Neuroscience). If you cannot meet this goal at that time, I will have to ask you to prepare to leave my lab by the end of August.


Monday, February 20, 2012

Reading Notes for Writing in the Sciences (Ch 05)

The Review Article

Research reviews typically present a synthesis of findings rather than a synthesis of view.

Direct quotations are rarely found in research reviews.

Review in this context means to synthesize or characterize a body of information, not simply to point out flows.

Locating the Literature

Research reviews focus on primary sources -- original reports of individual studies published in professional research journals -- as opposed to secondary sources such as textbooks or magazine articles written for non-expert audiences.

``forward'' from an article, by identifying other sources in which it was later cited.

Summaries and headlines from PLoS (

Reading Previous Research
  • What does the field already know about this topic?
  • What kinds of studies have been done?
  • What methods have been used, and how useful have they turned out to be?
  • What has been found?
  • What kind of information is till needed?
Identifying Trends and Patterns

The grid: research question, methods, and principal results

Organizing the Review
  • Introduce your discussion by establishing the significance of the topic
  • Organize the body of review to reflect the clusters or subtopics you have identified, using headings if the review is length.
  • Use topic sentences at the start of paragraphs and sections to highlight similarities and differences and points of agreement and disagreement.
  • Conclude with an overview of what is known and what is left to explore.
Citing Sources in the Text

The Council of Science Editors identifies three primary citation systems used in scientific journals: name-year, citation-sequence, and citation-name.

For works with more than two authors, use ``et al.'' or ``and others''

  • Ann M. Penrose, Steven B. Katz. Writing in the Sciences (3rd edition). Longman. 2009

Sunday, February 19, 2012

.bash_profile vs .bashrc

When you login (type username and password) via console, either sitting at the machine, or remotely via ssh: .bash_profile is executed to configure your shell before the initial command prompt.

If you’ve already logged into your machine and open a new terminal window, then .bashrc is executed before the window command prompt. .bashrc is also run when you start a new bash instance by typing /bin/bash in a terminal.

Most of the time you don’t want to maintain two separate config files for login and non-login shells. You can fix this by sourcing .bashrc from your .bash_profile file, then putting PATH and common settings in .bashrc. To do this, add the following lines to .bash_profile:

if [ -f ~/.bashrc ]; 
    then source ~/.bashrc

Now when you login to your machine from a console .bashrc will be called.


Saturday, February 18, 2012

SSH Tips

All changes are within file ~/.ssh/config

Multiple Connections

Often it’s useful to have multiple connections to the same server.

ControlMaster auto
ControlPath /tmp/ssh_mux_%h_%p_%r

Repeated Connections

If you find yourself making multiple consecutive connections to the same server then enablepersistent connections.

ControlPersist 4h


If currently you type a password when making an SSH connection, you can make connecting much more pleasant by setting up SSH keys.

$ ssh-keygen
$ ssh-copy-id

Hostname Aliases and Usernames

You can also define hostname aliases in SSH config, though this can involve listing each hostname. If your username on a remote server is different from your local username, specify this in your SSH config as well.

Host host1 host2 host3
   User username


Tuesday, February 14, 2012

Reading Notes for Writing in the Sciences (Ch 04)

  • introduction
  • methods and materials: past tense, active or passive voice
  • results: past tense
  • discussion
  • references
Common Moves in Research Article Introductions
  • establish topic and significance
  • establish need for present research
  • introduce the present research
Reporting Results
  • the major generalization(s) you are making about your data -- such generalizations are often stated in topic sentences at the beginning of paragraphs.
  • in pact form, the data supporting the generalization(s)
    • refer readers to the visual explicitly
    • tell them what patterns to notice
Discussion Trends and Implications
  • briefly summarize the major findings
  • acknowledge the advantages and limitations of the methods
  • explain the implications of the findings
  • outline the research questions that remain
Most Common Words
  • verbs: 
    • suggest, indicate, show, demonstrate
  • adverbs and adverbial phrases:
    • possibly, probably, very likely, necessarily, certainly, without doubt, presumably, in all probably, hypothetically, maybe, so far as the evidence suggests, as far as we can determine
  • modal auxiliary verb:
    • may, might, would, could, should, must, can, shall
  1. the topic will be introduced in present tense, usually in a sentence or two; 
  2. the background and/or need for the study will be outlined in another few sentences; 
  3. methods and results will be briefly described in past tense; and 
  4. the major conclusions and implications of the study will be stated in present tense.
How Scientists Read Reports
  • Readers typically began by scanning the title and abstract of an article and then looking for the data, focusing on the tables and graphs in which the data are summarized. Only after examining the data themselves did these scientists read the results sectin provided by the authors.
Checklist for Writers of Research Reports:
  • importance of the research
  • originality of the work
  • analysis of previous literature
  • appropriateness of the approach and experimental design
  • adequacy of experimental techniques
  • soundness of conclusions and interpretations
  • relevance of discussion
  • clarity of presentation and organization of the article
  • demonstration of reproducibility
  1. Ann M. Penrose, Steven B. Katz. Writing in the Sciences (3rd edition). Longman. 2009

Sunday, February 12, 2012

Noun Phrase Similarity Rules

  1. integer: [-+]?\d+
  2. rational number: \d+[/]\d+
  3. finite decimal representation: [-+]?[0-9]*[.][0-9]+([eE][-+]?[0-9]+)?
  4. suffix hyphen: \w+[-]
  5. prefix hyphen: [-]\w+
  6. infix hyphen: \w+[-]\w+
  7. [A-Z]{2,}
  8. [A-Z]+\d+
  9. [a-z]+\d+
  10. [a-z]+[A-Z]+
  11. [a-z]+[A-Z]+\d+
  12. [A-Z]+[a-z]+\d+
  13. [a-z]+\d+[A-Z]+
  14. [a-z]+\d+[a-z]+\d+
  15. [A-Z]+[a-z]+[A-Z]+\d+
  1. integer: [-+]?\d+
  2. rational number: \d+[/]\d+
  3. finite decimal representation: [-+]?[0-9]*[.][0-9]+([eE][-+]?[0-9]+)?
  4. suffix hyphen: \w+[-]
  5. prefix hyphen: [-]\w+
  6. infix hyphen: \w+[-]\w+
  7. [A-Z]{2,}
  8. [A-Z][\w \\\/-]*\d
  9. [a-z][\w \\\/-]*\d
  10. [a-z0-9]+[A-Z]+
  11. [a-zA-Z]+\d+[a-zA-Z]+
counter example of combining 3 and 4:  
p53 and TAFII40 and TAFII60

Wednesday, February 8, 2012

Tuesday, February 7, 2012

Varying Sentence Beginnings

1. Non-finite and verbless clause
1.1. gerund-participle
Using histidine - tagged recombinant TR6 , we screened soluble forms of TNF - ligand proteins with immunoprecipitation .

counter example:
Immunoblotting experiments indicate that GRB2 associates with ...

1.2. past-participle
Based on the experiences of all the authors , we emphasized cell cycle inhibitors such as p16 and p21 and regulators of apoptosis such as p53 and members of the bcl - 2 family .

1.3. to-infinitival
To examine whether GRB2 is also a component of ras signaling in mammalian cells , microinjection studies were performed .

2. dependent clause
As previously shown with reticulocyte lysate - reconstituted steroid receptor heteroprotein complexes , the reconstituted pp60 src multiprotein complex contains hsp70

Although both unstimulated and activated human T cells express high affinity IL - 7R , only activated T cells can proliferate to IL - 7 .

3. preposition phrase
In addition , hsp90 in the lysate complexes with wild - type pp60v - src .

From Scatchard analyses , the Kd :s for binding of aFGF and bFGF to hFGFR - 1 were estimated to 25 pM and 41 pM , respectively .

4. adverb
Interestingly , GRB2 exhibits striking structural and functional homology to the C. elegans protein sem - 5 .

5. noun phrase (an object)
The letter , I read it to to you.

  1. Rodney Huddleston, Geoffrey Pullum, etc. The Cambridge Grammar of the English Language. page 51,  604, 1173