Transcription factories in a Hela cell [from Cook PR (1999) Science 284, 1790]

Nuclear Structure and Function Research Group

Book / Writing tools
RESOURCES TO HELP YOU WRITE YOUR PAPERS (etc)

Teach yourself to touch type
Making a presentation
Giving a good talk
Building a website
Images of protein/DNA structures that you can rotate/print
DNA sequences, BLAST, genome browsers
Structures of chemicals
Molecular movies
Nomenclature, abbreviations
Citations, references
Dictionaries
Calculators online
Making dilutions of stock/radioactive solutions
Statistics
Physics, maths, macromolecular simulation, database of biological numbers
Writing an essay or paper
Classic books/articles on writing good prose
Grammars
Examination technique
Plagiarism
Responsible conduct in scientific research
Copyright
Resource for teachers of English for science
How to write a cv, get a job, build a career, etc.
Why scientific research is worth funding.

Teach yourself to touch type
Interactive tutorials.

Making a presentation
The basics from Wikiversity.
Improve digital image quality (from The Sheridan Group).
► Use in Figures of 'colour', 'salience', ' gestalt principles 1', 'typography', 'points of review (part 1)' and (part 2)', 'the overview figure', 'color blindness', 'avoiding color', 'arrows', 'layout', 'salience to relevance', 'design', 'data exploration', 'networks', 'integrating data', 'labels', 'axes', 'visual style', 'symbols', 'multidimensional data', 'storytelling' from B Wong and M Krzywinski. [Go to Nature Methods and search for 'Bang Wong' and 'M Krzywinski' to find more articles.]

Giving a good talk
Alon U. (2009). How to give a good talk. Mol. Cell 36, 165-167.

Building a website
Tips on how to build a web site, tutorials on HTML and JavaScript, etc.
How to build a web site.
World wide web consortium.

Images of protein/DNA structures that you can rotate/print
► Using software on your own computer, follow these steps:
Example: Green fluorescent protein (GFP).
1. Download a copy of 'RasMol'.  Go to http://www.umass.edu/microbio/rasmol/getras.htm and download the appropriate version for your computer (best to deposit the file in a directory you have made for the purpose).
2. Download the coordinates of GFP. Go to the PDB at http://www.rcsb.org/pdb/ and for 1gfl (one of the structures of the green fluorescent protein). [You can also view the structure through the web using one of the display options.] Select ''Download Files' on the left, choose the PDB file, and download it in PDB format into a directory that you have created.
3. Open 'RasMol'. Go to 'File' and open the appropriate .pdb file (eg 1GFL.pdb). If you want, you can now rotate the structure (under 'Settings', check 'Rotate Mol', and right click to rotate), change the 'Display' to 'Ribbons', or 'Copy' (or 'Export') the image into your paper or other drawing/presentation program.
Example: The nucleosome.
As above, but search for 1AOI.
Example: DNA double helix in the B form.
As above, but search for 1BNA.
Proteopedia: a web-based tool to look at proteins.

DNA sequences, BLAST, genome browsers
Learn to use the 'BLAST' algorithm (from Kerfeld and Scott).
A primer on genome annotation (from Yandell and Ence).
A primer by JR Hutchins telling you how you might analyze your gene or protein.
A trip to the genome browser at UCSC.

Structures of chemicals
Periodic Table from The Royal Society of Chemistry.
Periodic Table from WebElements.

Molecular movies
A portal to cell and molecular animations

Nomenclature, abbreviations
Chemical and biochemical nomenclature - IUPAC.
Nomenclature/styles/conventions/abbreviations from the Biochemical Journal.

Citations, references
Abbreviations of journals - PubMed.

Dictionaries
Merriam-Webster's - current American usage.
Oxford English dictionary - gives origins of words.
Multi-lingual general dictionary.

Calculators online
For calculations of all kinds.

Making dilutions of stock/radioactive solutions
Calculate volumes required for diluting stock solutions, how much radioactivity remains over time, etc..

Statistics
Statistics for biologists; choose the appropriate test; different tests.
Replicates and repeats from DL Vaux et al.
Error bars, error bars again, P values and t tests, in experimental biology.
► Go to PubMed, and search for 'Krzyywinski M' and you will find links to many useful primers.
A statistics texbook from Richard Lowry (Vassar), with worked examples.

Physics, maths, macromolecular simulation, database of biological numbers
Look at the index for a topic of interest (physics); from Georgia State.
Look at the index for a topic of interest (maths); from Georgia State.
Introduction to macromolecular simulation, by Peter J Steinbach.
Database of useful biological numbers.

Writing an essay or paper
From the University of Oxford.
The style guide from the 'Economist'.
Online writing lab from Purdue University.
A guide to grammar and style, by Jack Lynch.
Style guide from NCBI.
Tim Albert's tips for preparing your manuscript (from BioMed Central).
Wells, W.A. (2004).  Me write pretty one day: how to write a good scientific paper.  J. Cell Biol. 165, 757-758.
► Videos on how to publish a paper from the American Chemical Society: 1, 2,
A free online course in biomedical writing from Inter-Biotec.
For units of measurement, nomenclature, abbreviations, etc., from the Biochem. J.

Classic books/articles on writing good prose
'The King's English' by H. W. Fowler - old fashioned but correct English usage.
'Elements of style' by William Strunk - old fashioned but correct American usage.
Links to 'Politics and the English Language' by George Orwell, an essay on the uses/misuses of language.
Various texts on style and usage from Bartleby.

Grammars
A useful guide and on-line course from UCL.
By Anthony Hughes.

Examination technique
Writing essays - from the University of Indiana.

Copyright
From the University of Oxford.
An essay on copyright by Ronald B. Standler.
The US copyright office.

Plagiarism
From the University of Oxford.
From the University of Indiana.

Responsible conduct in scientific research
'On being a scientist: third edition' (2009). Sign on, and obtain free access to this book (from the National Academy of Sciences, USA) that discusses the responsibilites of scientists.
Rossner, M. & Yamada, K.M. (2004). What's in a picture? The temptation of image manipulation. J. Cell Biol. 166, 11-15.

Resource for teachers of English for science
By Jack Lynch.

How to write a cv, get a job, build a career
'How to' guides from Science magazine on writing a cv, handling an interview, getting a job, etc.
From the University of Indiana.
Yewdell, J.W. (2008). How to succeed in science: a concise guide for young biomedical scientists. Part I: taking the plunge. Nat. Rev. Mol. Cell Biol. 9, 413-416. [PubMed]
Yewdell, J.W. (2008). How to succeed in science: a concise guide for young biomedical scientists. Part II: making discoveries. Nat. Rev. Mol. Cell Biol. 9, 491-494. [PubMed]
Alon, U. (2010). How to build a motivated research group. Mol. Cell 37, 151-152. [PubMed]
Supervising undergraduates.
Supervising research students at Oxford.
'Creativity in graduate education' by Amanda Paulovich.
On why doing a Ph D is a waste of time (from the Economist).

Why scientific research is worth funding
Why science is worth funding (from WH Press).

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