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					How to Write a Paper

     Lecture One
                          ILOs

 Students will be able to;
     Identify common mistakes in submission.
     Find and follow guidelines for paper preparation.
     Use the rules to correctly reference papers and
      software in their own writing.
     Use the rules to correctly prepare figures for
      their own papers.
               Common Mistakes

 You do not want it to look like the final copy
  of the journal.
 A paper goes through a lot of stages before it
  is published (detailed on next slide)
 How they want the paper submitted is
  defined by the instructions to authors.
     You will find these on the journal webpages.
            Paper Publication Process

 Submission
      Send in the “raw paper” in a specified format.
 Refereeing
      Editors and Peers review the work for significance and “truth”.
 Corrections and Resubmission.
      No referee can think they have done their job with out suggesting
       corrections!
 Proofs
      Print ready copy of the article to check.
 Press – article actually appears.
                Instructions to Authors

 Define the Journal Scope.
      When submitting a paper you should send it to the
       appropriate journal.
          E.g. you would not send a paper on protein structure to a journal
           that looks at zoology.
 The overall format a paper can take is also defined.
      For example you can have Notes, Letters and full Papers.
      This defines the length of the paper.
                   Length of a Paper

   Given in instructions to authors.
   This is the length of the printed paper in the journal.
   This is not the length of the original manuscript.
   How long should the manuscript be?
       Depends of font size and spacing (see next slide).
       To work this out count the number of words in a typical
        printed journal page and in a manuscript page.
                   Font and Spacing

 Make it readable;
     Usually use Times New Roman font.
         I knew someone who would only ever use courier but
          that is madness.
     Never less than 11 point font.
     Double spaced or at least spacing and a half.
         This is so the referees can put on all those helpful
          comments.
              Instructions to Authors

 Define paper style.
      If it says you need an abstract divided into background,
       methods and results then you MUST do this.
      Follow them exactly – if you do not you fail at the first
       hurdle.
 Figures are not usually inserted into the paper.
      They are usually attached at the back.
      Figure legends are also often on a separate sheet from the
       figures.
      This is to do with how the journal prepares the paper.
                              Referencing

 This is defined in the instructions to authors.
      There are several different ways of doing this;
           Differences in what you put in the text body
           Differences in what you put in the reference section.
      If it is not clear in the instructions to authors try and find
       a recent article from the journal and copy that style.
      If they say something you have to do it.
           Even if it means finding the titles of all the papers!
                 Referencing Example

 Bioinformatics;
      In the text cited by author and date.
          (Dalby, 2001)
      Not more than 2 authors cited per reference in the text.
          (Dalby & Littlechild, 2001) or (Dalby and Littlechild, 2001)
          Check whether & or and is used.
          But not (Dalby, Isupov, Littlechild, 2001)
      For more than 2 authors et al. should be used.
          (Dalby et al., 2001) for the above reference.
                 Referencing Example

 Bioinformatics ctd.
      At the end of the manuscript citations should be given in
       alphabetical order.
      Format should be;
          Surname
          Initial
          Year
          Paper title
          Journal title
          Volume
          Page numbers for start and finish
                 Referencing Example

 Bioinformatics ctd.
      Bryce, C.F.A. (1982) Rapid nucleic acid sequencing
       methods – alternative approaches to facilitating learning.
       J. Biol. Educ., 16, 275-280.
      Notes.
          Date in curved brackets.
          Journal title in italics.
          Journal title abbreviated according to World List of Scientific
           Periodicals.
          Volume number in bold.
             Referencing Example

 Bioinformatics ctd.
     Soll, D. and Roberts, R.J. (1984) The
      Applications of Computers to Research on
      Nucleic Acids II Part 2. IRL Press, Oxford.
     Notes
       This is a book citation.
       Title in italics.

       Needs publisher and address.
                 Referencing Example

 Bioinformatics ctd.
      Lonsdale, D.M., Hodge, T.P., and Stoehr, P.J. (1984) A
       computer program for the management of small cosmid
       banks. In Soll, D. and Roberts, R.J. (eds), The
       Applications of Computers to Research on Nucleic Acids
       II Part 2. IRL Press, Oxford, pp. 429-436.
      Notes
          This is a chapter reference.
          Note the use of commas for a list of authors.
          The page numbers of the chapter go at the end.
            Referencing Software

 Most – if not all software will have an
  associated paper.
     You have to reference this when you cite the
      software.
     This does not mean that you have read the paper.
     You can usually find the correct reference from
      the manual for the program.
       General Rule for Referencing

 Would someone think that what you have described
  was your work?
     If they would and you are referring to someone else’s
      work it has to be referenced.
     Depending on journal submission rules references can
      either be to where the “result” from someone else’s work
      is made or at the end of the sentence containing it.
     The best way of getting experience of this is reading
      papers.
       Referencing Database Entries

 This is very subjective;
     If the database itself is the essential part then the
      reference for the entire database should be given.
         Again this will usually be given on the database
          webpages.
     If only a few entries are the critical part then the
      papers that refer to them should be referenced.
         These will often be listed in the database entries.
      Referencing Database Entries

 In your mini-project;
     Many sequences from EMBL.
         Reference for EMBL is appropriate.
     Few protein structures used to make the model.
         Reference for PDB and probably each of the entries
          should be included.
     One or two proteins used for structural
      comparison.
         Reference to the structural paper must be given.
                                Figures

 Should follow submission guidelines;
      Already said they are attached at the back.
      They should be clear.
          This can depend on format.
      They should NOT be reduced to the size they will appear
       in the paper.
      They should have appropriate labels within the figures if
       required.
      They should have accompanying keys if required.
                             Figures

 Should have figure number written on the back in
  pencil.
 Legends should be on a separate sheet.
 There should be an indication in the text (often
  written in pencil) as to where the figures should go.
 There should be the necessary references to the
  figures within the text.
      E.g. (see fig. 9) or as described in figure 9 or …
                    Reusing Figures

 Would have to be copyright cleared by the
  authors and publisher of the original paper.
     Then you would state;
     “Reproduced from XXXX figure used with
      permission”
         Or something along these lines.
 If in doubt you have to make your own!
Writing a Literature Review

        Lecture Two
                           ILOs

 Students will consider;
     Why we review.
     What makes a good review.
     How to write a review.
     How to use the literature effectively.
      Writing a Literature Review

 What does a review contribute to the
  community?
 Why do we do them?
 Who writes them?
 Who uses them?
 Are they just parasitic publications that use
  other peoples results?
      Who Writes and Who Reads?

 Who writes?
     Experts in the field.
     Usually invited articles.
     Someone with years of experience in that
      subject.
 Who uses them?
     Students
     Those who need “quick access” to a field.
             What is a Good Review

 A good review should be a synthesis of the subject.
      The whole should be more than the sum of the parts.
      By using information from all the papers and relating it
       to one another you should get a more complete picture of
       the subject.
 A bad review is a mere collection of snippets or
  quotes.
      In this case there is no analysis – it does not go beyond
       the original papers.
                Writing a Review

 Should sample the literature appropriately.
     Appropriately depends on what you are doing.
     You do not want to be too broad or you will have
      far too much to read.
     You do not want to be too narrow or you will
      have very little literature.
     If in doubt go for broader.
               Finding the Literature

 Web of Science.
      This should be your first place to search for papers on a
       particular subject.
 Medline
      In case WOS missed something.
 Bioinformatics Databases.
      In case the search over-whelmed you with results.
      This could add some focus.
                      Selectivity

 This is the most important skill of a
  researcher.
 This comes with experience.
     Experience both in;
       Reading papers.
       Writing papers.

 Knowledge is always imperfect – there is
  always an element of the subjective.
                 Abstracts or Papers

 Web of Science will give you the abstracts of all the
  papers that result from your search.
      Use these to reduce the literature and to focus on the
       papers that are most relevant.
      We have a poor library so consider journals that we have
       access to as well as the significance of the paper’s
       content.
 Can you get away with just the abstract?
      If the abstract gives you enough information about the
       content of the paper do you need to get the paper?
                  Reading Papers

 Information overload.
     There are a lot of papers with a lot of facts but
      even if the paper is relevant not all of the paper
      will be.
     You should practice getting the gist of a paper.
     Part of writing a review is being able to
      effectively précis the papers you read.
     This is to find the significant parts of the paper.
                 Reading Papers

 Papers almost always have the following
  sections;
     Abstract
     Background.
     Methods.
     Results and discussion.
     Conclusions.
 Which are the most important parts to read?
           Paraphrase of Bacon

 Some papers are to be tasted, others to be
  swallowed and some few to be chewed and
  digested; that is some papers are to be read
  only in parts; others to be read but not
  curiously and some few to be read wholly,
  and with diligence and attention.
                            Of studies – F Bacon
                     Reading Papers

 Abstract.
      Often saves you the time of reading the whole thing.
      Should be read to make sure it is relevant.
      Should give a summary of the content.
 Background.
      Can be useful if you are new to the subject.
      Useful resource for other materials.
      Should not be chewed and digested
                     Reading Papers

 Methods.
      Should be ignored unless you are going to do something
       very similar.
      From this you are supposed to be able to repeat the
       experiment – not often the case.
 Results and Discussion..
      The bit you care about most.
      This tells you the reason for the paper and what was
       discovered.
                     Reading Papers

 Results and Discussion.
      Keep in mind what can be checked.
      Keep in mind other results in other papers.
      Is there a consistent picture?
 Conclusions.
      To be lightly tasted at most.
      Can be highly subjective – opinion.
      Can be limited to reaffirmation of discussion.
                 Citations in the text

 For reviews citations can get repetitive and so you
  need to use variations.
 Either you state the facts from the paper and then
  put the references in brackets at the end of the
  sentence or you could use the following;
 Dalby and Littlechild showed that …(Dalby and
  Littlechild, 2001).
      Note that even when you state the names you still need to
       state the reference.
                        Use of Italics

   Genotypes should be given in italics.
   Phenotypes should not be in italics.
   Gene names are also commonly in italics.
   Species names must always be in italics.
   Species names should be given in full the first time
    they are used.
       E.g. Escherichia coli which becomes E. coli in later
        references.

				
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