2014-9-24-SBC361-ResearchMethComm
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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.
![• 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](https://image.slidesharecdn.com/2014-9-24-sbc361-researchmethcomm-140926052729-phpapp01/85/2014-9-24-SBC361-ResearchMethComm-41-320.jpg)
![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”](https://image.slidesharecdn.com/2014-9-24-sbc361-researchmethcomm-140926052729-phpapp01/85/2014-9-24-SBC361-ResearchMethComm-46-320.jpg)
![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](https://image.slidesharecdn.com/2014-9-24-sbc361-researchmethcomm-140926052729-phpapp01/85/2014-9-24-SBC361-ResearchMethComm-47-320.jpg)
![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](https://image.slidesharecdn.com/2014-9-24-sbc361-researchmethcomm-140926052729-phpapp01/85/2014-9-24-SBC361-ResearchMethComm-48-320.jpg)
![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](https://image.slidesharecdn.com/2014-9-24-sbc361-researchmethcomm-140926052729-phpapp01/85/2014-9-24-SBC361-ResearchMethComm-51-320.jpg)
![“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](https://image.slidesharecdn.com/2014-9-24-sbc361-researchmethcomm-140926052729-phpapp01/85/2014-9-24-SBC361-ResearchMethComm-53-320.jpg)
![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](https://image.slidesharecdn.com/2014-9-24-sbc361-researchmethcomm-140926052729-phpapp01/85/2014-9-24-SBC361-ResearchMethComm-67-320.jpg)
2014-9-24-SBC361-ResearchMethComm
- 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
- 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() ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 120 80 40 0 5 10 15 20 speed dist Figure 1: A scatterplot of cars