This document provides guidance on writing skills and best practices for research methods and communications. It discusses writing different types of documents like essays, cover letters, and dissertations. It provides a marking scheme for essay-style questions and criteria for different grade levels. It offers tips for structuring writing clearly with separate introduction, one paragraph per idea, and smooth transitions. The document also discusses using functions and loops in R programming and gives examples. Finally, it promotes practices like reproducible research, sustainable software, and taking notes in Markdown.

1. Research Methods & Comms.
y.wurm@qmul.ac.uk
http://yannick.poulet.org

2. Writing
• an essay!
• a cover letter!
• a reference letter!
• (a “new scientist article”)!
• a dissertation!
• (an abstract)

3. QMUL marking scheme Marking Criteria and Mark Scheme for Essay-style Questions
Levels 5 - 6 Level 6
All Levels
(Desirable in other years)
Evidence of Comprehension Breadth and Depth of Knowledge Irrelevant Material and Errors Synthesis & Balance Originality & Innovation
A+ Outstanding. Deep insight
Outstanding. As much as could be
expected
Absent or minimal Evidence of critical analysis Original ideas and insight
Clear understanding. Shrewd and
appropriate
Extensive. Almost as much as could be
expected
Minimal or absent Astute selection and juxtaposition Some evidence of creative A- Tending to description rather than
interpretation
Extensive Minimal Appropriate selection and combination Some
A-- Sufficient to marshal a well-organised,
direct response
Most key points but not extensive
Perhaps some minor errors and tangential
material
Inappropriate balance, partial synthesis Limited
Sufficient to marshal an organised, direct
response
Not all key points but comprehensive and
accurate
Some minor errors and tangential material Inappropriate balance, partial synthesis Limited
Not a direct response but sufficient for a
logical presentation.
Several omissions but some key points Some errors, tangential material Minimal Minimal
D,E Poor comprehension, muddled
organisation
Major omissions. No key points. A few
basic facts
Major factual errors. Frequently irrelevant None None
F+ Almost none One or two very minor points correct Extensively irrelevant or wrong None None
None
One or two very minor points just about
correct
Extensively irrelevant or wrong None None
F- None No evidence of being better if longer Almost all irrelevant or wrong None None
Nothing written Nothing written Nothing written None None
Notes:
x In order to qualify for an "A-grade" the work must meet most of the indicated criteria.
x Grade to % conversion: A+ = 100; A = 92; A- = 83; A-- = 74; B+ = 68; B = 65; B- = 63; C+ = 58; C = 55; C- = 53; D+ = 49; D = 48; D- = 47; E+ = 44; E = 43; E- = 42; F++ = 39; F+ = 37; F = 27; F- = 17; 0 = 0

4. Important for all: Structure
Clear overall structure?!
Separate intro!
starts from general points.!
announces the structure (paragraphs or major
sections).!
One paragraph per idea/point.!
Clear structure within each paragraph. !
If includes a list: “three lines of evidence suggest
that X. First, ...., Second, ... Finally....”!
Clarity of each sentence.!
No unnecessary words!!
Try to make smooth transitions

5. More writing tips.
• No ping-ponging!!
• Consider carefully: what is boring? what is sexy? what is
necessary? what can be simplified? !
• ELIMINATE unnecessary ideas. !
• Eliminate unnecessary words: shorter is better!
• “We have performed X” -- “We X-ed”!
• Put MS Word in “strict grammar” mode.!
• Eliminate jargon. !
• write for the “general smart scientists” with little domain
specific knowledge.

7. © Alex Wild others

9. Atta leaf-cutter ants
© National Geographic

10. Atta leaf-cutter ants
© National Geographic

11. Atta leaf-cutter ants
© National Geographic

13. Oecophylla Weaver ants
© ameisenforum.de

14. © ameisenforum.de
Fourmis tisserandes

15. © ameisenforum.de
Oecophylla Weaver ants

16. © wynnie@flickr © forestryimages.org

17. Tofilski et al 2008
Forelius pusillus

18. Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

19. Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

20. Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

21. Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

22. Forelius pusillus hides the nest entrance at night
Avant
Workers staying outside die
« preventive self-sacrifice »
Tofilski et al 2008

23. Dorylus driver ants: ants with no home
© BBC

24. Animal biomass (Brazilian rainforest)
Mammals
Birds
Reptiles
Other insects Amphibians
from Fittkau Klinge 1973
!
Earthworms
!
!
Spiders
Soil fauna excluding
earthworms,
ants termites
Ants termites

25. We use modern technologies to
understand insect societies.!
• evolution of social behaviour!
• molecules involved in social behaviour!
• consequences of environmental change

27. More career stuff
• Internships?!
•What does PhD mean?!
• Basic CV rules

29. Consultation TODAY!
11a.m. to 2p.m.!
Library Square

30. Consultation TODAY!
11a.m. to 2p.m.!
Library Square

31. Big data is invading biology

32. This changes
454! everything.
Illumina!
Solid...
Any lab can
sequence
anything!

33. Big data is invading biology
• Genomics!
• Biodiversity assessments!
• Stool microbiome sequencing!
• Personalized medicine!
• Cancer genomics!
• Sensor networks - e.g tracking microclimates, recording sounds!
• Aerial surveys (Drones) - e.g. crop productivity; rainforest cover!
• Camera traps

35. Learning to deal with big data takes time
• New Master’s Programs @ QM: !
• Bioinformatics (for biologists)!
• Ecological Evolutionary Genomics (or Biodiversity Informatics)!
• Our 8 hours of practicals.

37. Practicals
• Aim: get relevant data handling skills!
• Doing things by hand: !
• impossible? !
• slow, !
• error-prone, !
• Automate!!
• Basic programming!
• in R!
• no stats!

38. Practicals: contents
• Groups - ok?!
• First 3h practical!
• data accessing/subsetting!
• search/replace!
• regular expressions
• Second 3h practical!
• functions
• loops!
• Third session: !
Text search on steroids
Reusable pieces of work
Repeating the same thing many times
• 1.5h practical (integrating revising all skills)!
• 1.5h exam

40. http://tryr.codeschool.com
chapters 1 to 6

41. • creating a vector
• give me a vector containing numbers from 5 to 11 (3 variants)
myvector - 5:11
myvector - seq(from=5, to=11, by=1)
myvector - c(5, 6, 7, 8, 9, 10, 11)
myvector
[1] 5 6 7 8 9 10 11
• accessing a subset
• of a vector
bigvector - 150:100
bigvector
[1] 150 149 148 147 146 145 144 143 142 141 140 139 138 137 136 135 [20] 131 130 129 128 127 126 125 124 123 122 121 120 119 118 117 116 [39] 112 111 110 109 108 107 106 105 104 103 102 101 100
mysubset - bigvector[myvector]
mysubset
[1] 146 145 144 143 142 141 140
!
subset(bigvector, bigvector 120)
[1] 150 149 148 147 146 145 144 143 142 141 140 139 138 137 136 135 [20] 131 130 129 128 127 126 125 124 123 122 121

45. Regular expressions (regex): !
Text search on steroids.

46. Regular expressions (regex): !
Text search on steroids.
Regular expression Finds
David David
Dav(e|(id)) David, Dave
Dav(e|(id)|(ide)|o) David, Dave, Davide, Davo
At{1,2}enborough Attenborough,
Atenborough
Atte[nm]borough Attenborough,
Attemborough
At{1,2}[ei][nm]bo{0,1}ro((ugh)|w){0,1}
Atimbro,
attenbrough,!
ateinborow
Easy counting, replacing all with “Sir David Attenborough”

47. Regex Special symbols
Regular expression Finds Example
[aeiou] any single vowel “e”
[aeiou]* between 0 and infinity
vowels vowels, e.g.’ “eeooouuu
[aeoiu]{1,3} between 1 and 3 vowels “oui”!
!
a|i one of the 2 characters “
((win)|(fail)) one of the two
words in () fail

48. More Regex Special symbols
Synonymous with
[:digit:] [0-9]
[A-z] [A-z], ie [A-Za-z]
s whitespace
. any single character
.+ one to many of anything
b* between 0 and infinity letter ‘b’
[^abc] any character other than a, b or c.
( (
[:punct:] any of these: ! # $ % ' ( ) * + , - . /
: ; = ? @ [ ] ^ _ ` { |
• Google “Regular expression cheat sheet”!
• ?regexp

50. Functions

51. Functions
• R has many. e.g.: plot(), t.test()!
• Making your own:
tree_age_estimate - function(diameter, species) {
[...do the magic... maybe something like:
growth.rate - growth.rates[ species ]
age.estimate - diameter / growth.rate
...]
!
return(age.estimate)
}
tree_age_estimate(25, “White Oak”)
+ 66
tree_age_estimate(60, “Carya ovata”)
+ 190

52. Loops

53. “for”
Loop
possible_colours - c('blue', 'cyan', 'sky-blue', 'navy blue',
'steel blue', 'royal blue', 'slate blue', 'light blue', 'dark
blue', 'prussian blue', 'indigo', 'baby blue', 'electric blue')
!
possible_colours
[1] blue cyan sky-blue navy blue
[5] steel blue royal blue slate blue light blue
[9] dark blue prussian blue indigo baby blue
[13] electric blue
!
for (colour in possible_colours) {
+ print(paste(The sky is oh so, so, colour))
+ }
!
[1] The sky is so, oh so blue
[1] The sky is so, oh so cyan
[1] The sky is so, oh so sky-blue
[1] The sky is so, oh so navy blue
[1] The sky is so, oh so steel blue
[1] The sky is so, oh so royal blue
[1] The sky is so, oh so slate blue
[1] The sky is so, oh so light blue
[1] The sky is so, oh so dark blue
[1] The sky is so, oh so prussian blue
[1] The sky is so, oh so indigo
[1] The sky is so, oh so baby blue
[1] The sky is so, oh so electric blue

54. Test

57. Jasmin Zohren Maïté Guignard Kim Warren
Bruno
Vieira
Rodrigo
Pracana
Leandro
Santiago
James
Borrell

58. Reproducible Research,!
Sustainable Software!
Scientific Computing

59. Why care?

62. Aquaculture in
Offshore Zones
LETTERS I BOOKS I POLICY FORUM I EDUCATION FORUM I PERSPECTIVES
operations that reveal little, if any, negative
impact on the environment or local ecosys-tems
(2, 3). Naylor criticizes the National
industry governed by regulations with a rational
basis in the ecology of the oceans and the eco-nomic
realities of the marketplace.
1878
in the classroom
1880 1882
perspectives
LETTERS
edited by Etta Kavanagh
Retraction
WE WISH TO RETRACT OUR RESEARCH ARTICLE “STRUCTURE OF
MsbA from E. coli: A homolog of the multidrug resistance ATP bind-ing
cassette (ABC) transporters” and both of our Reports “Structure of
the ABC transporter MsbA in complex with ADP•vanadate and
lipopolysaccharide” and “X-ray structure of the EmrE multidrug trans-porter
in complex with a substrate” (1–3).
The recently reported structure of Sav1866 (4) indicated that our
MsbA structures (1, 2, 5) were incorrect in both the hand of the struc-ture
and the topology. Thus, our biological interpretations based on
these inverted models for MsbA are invalid.
An in-house data reduction program introduced a change in sign for
anomalous differences. This program, which was not part of a conven-tional
data processing package, converted the anomalous pairs (I+ and
I-) to (F- and F+), thereby introducing a sign change. As the diffrac-tion
data collected for each set of MsbA crystals and for the EmrE
crystals were processed with the same program, the structures reported
in (1–3, 5, 6) had the wrong hand.
The error in the topology of the original MsbA structure was a con-sequence
of the low resolution of the data as well as breaks in the elec-tron
density for the connecting loop regions. Unfortunately, the use of
the multicopy refinement procedure still allowed us to obtain reason-able
refinement values for the wrong structures.
The Protein Data Bank (PDB) files 1JSQ, 1PF4, and 1Z2R for
MsbA and 1S7B and 2F2M for EmrE have been moved to the archive
of obsolete PDB entries. The MsbA and EmrE structures will be
recalculated from the original data using the proper sign for the anom-alous
differences, and the new Ca coordinates and structure factors
will be deposited.
We very sincerely regret the confusion that these papers have
caused and, in particular, subsequent research efforts that were unpro-ductive
as a result of our original findings.
GEOFFREY CHANG, CHRISTOPHER B. ROTH,
CHRISTOPHER L. REYES, OWEN PORNILLOS,
YEN-JU CHEN, ANDY P. CHEN
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
References
1. G. Chang, C. B. Roth, Science 293, 1793 (2001).
2. C. L. Reyes, G. Chang, Science 308, 1028 (2005).
3. O. Pornillos, Y.-J. Chen, A. P. Chen, G. Chang, Science 310, 1950 (2005).
4. R. J. Dawson, K. P. Locher, Nature 443, 180 (2006).
5. G. Chang, J. Mol. Biol. 330, 419 (2003).
6. C. Ma, G. Chang, Proc. Natl. Acad. Sci. U.S.A. 101, 2852 (2004).
Downloaded from www.sciencemag.org on September 24, 2014

63. Some sources of inspiration

66. Take notes in Markdown “compile”!
to html, pdf,

67. knitr (sweave)Analyzing Reporting in a single file.
analysis.Rmd
A minimal R Markdown example
I know the value of pi is 3.1416, and 2 times pi is 6.2832. To compile library(knitr); knit(minimal.Rmd)
A paragraph here. A code chunk below:
1+1
## [1] 2
### in R:
library(knitr)
knit(“analysis.Rmd”)
# -- creates analysis.md
### in shell:
pandoc analysis.md -o analysis.pdf
# -- creates MyFile.pdf
.4-.7+.3 # what? it is not zero!
## [1] 5.551e-17
Graphics work too
library(ggplot2)
qplot(speed, dist, data = cars) + geom_smooth()
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120
80
40
0
5 10 15 20 speed
dist
Figure 1: A scatterplot of cars