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.