Peter R Cook's Nuclear Structure and Function Research Group

RESOURCES TO HELP YOU WRITE YOUR PAPERS (etc)

• Teach yourself to touch type
• Making a presentation
• Building a website
• Images of protein/DNA structures that you can rotate/print; using databases, BLAST
• 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
• Giving a good talk
• How to write a cv, get a job, build a career, etc.

Teach yourself to touch type
► Interactive tutorials.

Making a presentation
► The basics from Wikiversity.
► Some advice from Swarthmore.
► Check and improve digital image quality - a free service provided by The Sheridan Group; these pages also provide good information on the different formats/color systems/etc used.
► 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' from B Wong. [Go to Nature Methods and search for 'Bang Wong' to find more articles.]

Building a website
► Tips on how to build a web site, tutorials on HTML and JavaScript, etc.
► How to build a web site.
► Understanding HTML
► Tidy up your HTML code.
► World wide web consortium.

Images of protein/DNA structures that you can rotate/print; using databases, BLAST
If you wish to view a protein or DNA structure, or include one in a paper, 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.
► Download a copy of 'Protein Expolorer'; this enables you to do the same things (and more) that you can do with 'Rasmol'.
► Pages on molecular modeling.
► Tutorials on X-ray crystallography, and on which graphics software to use.
► Learn to use the 'BLAST' algorithm (from Kerfeld and Scott).

Structures of chemicals
► Find the structure of chemicals, examine (e.g. rotate) them using 'ChemDraw' (download free copy), and draw new ones using 'Isis/Draw' (free copy).
► Periodic Table.

Molecular movies
► A portal to cell and molecular animations

Nomenclature, abbreviations
► Biochemical nomenclature - IUPAC.
► IUPAC rules for use of italic and roman fonts for symbols in scientific text.
► IUPAC list of quantities, units and symbols in physical chemistry.
► Nomenclature/styles/conventions/abbreviations from the Biochemical Journal.

Citations, references
► Abbreviations of journals - Chemical Abstracts.
► Abbreviations of journals - Biological Abstracts.
► Abbreviations of journals - PubMed.

Dictionaries
► Cell and molecular biology.
► 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.
► Error bars in experimental biology.
► 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.

Plagiarism
► From the University of Oxford.
► From Princeton University.
► From the University of Indiana.
► JISC plagiarism advisory service.

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.

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

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 research students at Oxford.

	Nuclear Structure and Function Research Group
	Peter R Cook's group at The Sir William Dunn School of Pathology University of Oxford
	Home Our science Publications Images Students Book
Quick links Contacts, visiting Oxford Model for all genomes EpiGenSys Students: Lecture notes Reading lists Resources Movies: 1. Transcription cycle 2. Mobile/fixed polymerases? Catalogs: 1. Proteomes of factories 2. Engaged polymerases	Book / Writing tools
	RESOURCES TO HELP YOU WRITE YOUR PAPERS (etc) • Teach yourself to touch type • Making a presentation • Building a website • Images of protein/DNA structures that you can rotate/print; using databases, BLAST • 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 • Giving a good talk • How to write a cv, get a job, build a career, etc. Teach yourself to touch type ► Interactive tutorials. Making a presentation ► The basics from Wikiversity. ► Some advice from Swarthmore. ► Check and improve digital image quality - a free service provided by The Sheridan Group; these pages also provide good information on the different formats/color systems/etc used. ► 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' from B Wong. [Go to Nature Methods and search for 'Bang Wong' to find more articles.] Building a website ► Tips on how to build a web site, tutorials on HTML and JavaScript, etc. ► How to build a web site. ► Understanding HTML ► Tidy up your HTML code. ► World wide web consortium. Images of protein/DNA structures that you can rotate/print; using databases, BLAST If you wish to view a protein or DNA structure, or include one in a paper, 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. ► Download a copy of 'Protein Expolorer'; this enables you to do the same things (and more) that you can do with 'Rasmol'. ► Pages on molecular modeling. ► Tutorials on X-ray crystallography, and on which graphics software to use. ► Learn to use the 'BLAST' algorithm (from Kerfeld and Scott). Structures of chemicals ► Find the structure of chemicals, examine (e.g. rotate) them using 'ChemDraw' (download free copy), and draw new ones using 'Isis/Draw' (free copy). ► Periodic Table. Molecular movies ► A portal to cell and molecular animations Nomenclature, abbreviations ► Biochemical nomenclature - IUPAC. ► IUPAC rules for use of italic and roman fonts for symbols in scientific text. ► IUPAC list of quantities, units and symbols in physical chemistry. ► Nomenclature/styles/conventions/abbreviations from the Biochemical Journal. Citations, references ► Abbreviations of journals - Chemical Abstracts. ► Abbreviations of journals - Biological Abstracts. ► Abbreviations of journals - PubMed. Dictionaries ► Cell and molecular biology. ► 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. ► Error bars in experimental biology. ► 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 ► An essay on copyright by Ronald B. Standler. ► The US copyright office. Plagiarism ► From the University of Oxford. ► From Princeton University. ► From the University of Indiana. ► JISC plagiarism advisory service. 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. Giving a good talk ► Alon U. (2009). How to give a good talk. Mol. Cell 36, 165-167. 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 research students at Oxford. Top \| Home \| Maintained by Peter Cook \|

Nuclear Structure and Function Research Group

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