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Principles of Nuclear  
Structure and Function  

Peter R. Cook

Online Writing Tools   
Teach yourself to touch type 
http://www.learn2type.com/ Interactive tutorials. 

Using Microsoft 'Word' 
http://www.counsell.com/ Go to 'Word for the wise' (by Damian Counsell) - a primer on how to use the program to write your thesis. 

Making a presentation 
http://einstein.cs.uri.edu/tutorials/csc101/powerpoint/ppt.html Tutorial on how to use Microsoft 'Powerpoint' from The University of Rhode Island. 
http://staff.philau.edu/bells/ppt.html Another guide with lots of links. 

Guidelines for building a website 
http://www.ox.ac.uk/webhelp Guidelines and links provided by the University of Oxford. 

Images of protein/DNA structures that you can rotate/print 
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' from the Protein Data Bank (PDB). Go to http://www.rcsb.org/pdb/, then 'Links', 'Software, and 'Molecular Graphics'; choose 'RasMol', 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 choose 'SearchLite'; search for 'green fluorescent protein', and select the variant you want (eg 1GFL). [Select 'View Structure' and 'Ribbons' or 'Cylinders' to see images that you can save after right clicking on the image.] Select 'Download/Display File', and 'Download the structure file' in PDB format without compression (if you so wish) in to the directory 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 in 'SearchLite' search for 'nucleosome', and get the appropriate .pdb file (eg 1AOI) 
Example: DNA double helix in the B form. 
As above, but in 'SearchLite' search for 'B-DNA dodecamer', and get an appropriate .pdb file (eg 1BNA). 

Structures of chemicals 
Find the structure of chemicals at http://nci.chemfinder.com/nci99/index.asp, examine (e.g. rotate) them using 'ChemDraw' (download free copy), and draw new structures using 'Isis/Draw' (download free copy). 
http://www.webelements.com/ Periodic Table. 

Nomenclature, abbreviations 
http://www.chem.qmw.ac.uk/iupac/index.html Biochemical nomenclature - IUPAC. 
http://www.iupac.org/standing/idcns/fonts_for_symbols.html IUPAC rules for use of italic and roman fonts for symbols in scientific text. 
http://www.iupac.org/reports/1993/homann/index.html IUPAC list of quantities, units and symbols in physical chemistry. 

Citations, references 
http://www.cas.org/sent.html Abbreviations of journals - Chemical Abstracts. 
http://hsc.usf.edu/bja/ Abbreviations of journals - Biological Abstracts. 
http://www.ncbi.nlm.nih.gov:80/entrez/journals/loftext_noprov.html Abbreviations of journals - PubMed. 

Dictionaries 
http://on.to/dictionary Cell and molecular biology. 
http://bioinformatics.weizmann.ac.il/hotmolecbase/ 'Hot' molecules in biomedicine. 
http://biotech.icmb.utexas.edu/pages/dictionary.html Life sciences. 
http://www.m-w.com/dictionary Merriam-Webster's - current American usage. 
http://dictionary.oed.com/entrance.dtl Oxford English dictionary - gives origins of words. 
http://www.facstaff.bucknell.edu/rbeard/diction.html Multi-lingual general dictionary. 

Calculators online 
http://www-sci.lib.uci.edu/HSG/RefCalculators.html For calculations of all kinds. 

Writing an essay or paper 
http://ccc.commnet.edu/grammar/ A guide to composition, grammar, and writing. 
http://owl.english.purdue.edu/ Online writing lab from Purdue University. 
http://andromeda.rutgers.edu/~jlynch/Writing/ A guide to grammar and style, by Jack Lynch. 
http://filebox.vt.edu/eng/mech/writing/ Technical/scientific writing, from Virginia Tech. 

Classic books/articles on writing good prose 
http://www.bartleby.com/116/ 'The King's English' by H. W. Fowler - old fashioned but correct English usage. 
http://www.bartleby.com/people/Strunk-W.html 'Elements of style' by William Strunk - old fashioned but correct American usage. 
http://www.bartleby.com/64/ The American Heritage® Book of English Usage - current American usage. 
http://www.resort.com/~prime8/Orwell/ Links to 'Politics and the English Language' by George Orwell, and essay on the uses and misuses of language. 
http://www.bartleby.com/usage/ Various texts on style and usage from Bartleby. 

Grammars 
http://www.edunet.com/english/grammar/ By Anthony Hughes. 
http://ccc.commnet.edu/grammar/ By Charles Darling. 

Examination technique 
http://www.indiana.edu/~wts/wts/essayexam.html Writing essays - from the University of Indiana. 

Plagiarism 
http://www.rbs2.com/plag.htm An essay on plagiarism by Ronald B. Standler. 
http://www.indiana.edu/~wts/wts/plagiarism.html From the University of Indiana. 
http://sja.ucdavis.edu/sja/plagiarism.html From the University of California at Davis. 
http://www.arts.ubc.ca/doa/plagiarism.htm From the University of British Columbia. 

Copyright 
http://www.rbs2.com/copyr.htm An essay on copyright by Ronald B. Standler. 
http://lcweb.loc.gov/copyright/ The US copyright office. 

Resource for teachers of English for science 
http://andromeda.rutgers.edu/~jlynch/Writing/links.html By Jack Lynch. 
 

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