10+ general rules
- The report/essay should be easy to read, clear and logical.
- Use short, simple sentences, ideally less than 20 words each.
- Start with a general outline: Introduction, Methods (normally not in a review), Results, Discussion, Conclusion (optional).
- Delete what is not necessary. Good style is more important (and gets a better mark) than the word count.
- Ask yourself: what do you want to say? What do you want to tell your reader? If written this way, would you have understood it 3 months ago?
- Each factual statement must either refer to another source or to your own data. Do not plagiarise.
- Unless you are very, very experienced, avoid intimate and personal comments, as well as funny remarks and jokes.
- Use a spell chceker, Luke.
- Do not plagiarise (see below)!!
- Reading these rules is not a substitute for reading this whole page.
- - 100. DO NOT PLAGIARISE!!! *NEVER, UNDER NO CIRCUMSTANCES*!!!!!!
Writing an essay or a report is amongst the most important tasks in science. Unfortunately, it is still badly neglected in many curricula.
Consider that science is always about how you express yourself and how you contribute to an ongoing debate, very rarely insights or findings are completely "de novo" and "ex nihilo". So, whatever you do or want to report on, is a part of an ongoing discussion. Consequently, the presentation (and this does not primarily refer to the layout) is extremely important. This includes easy to understand figures, a clear and logical structure (which itself is sort of a language people have agreed upon) and a clear and precise language.
In other words: be scholarly and remember you are always standing on the shoulders of giants!
In the following we want to give you some guidelines which should help you write reports. However, writing reports and essays is much like learning a language: you can only learn it through practise. Theoretical knowledge is helpful to get started and to reflect on your own capabilities and skills, but it can only be a guideline - not more. And, at the end of the day, there is also no point in thinking too much about it: just do it, trial and error is often your best teacher.
A report or essay is structured as follows: Title, Name and Affiliation, Abstract, Introduction, Methods (normally not present in an essay), Results, Discussion, Conclusions (optional) References, each headed by an appropriate subtitle.
2.1. ABSTRACT: should be a short statement summarising the most important facts and conclusions from the work. It should spare any details and be limited to typically 150-250 words (5-10 sentences). It is not a table of contents but should explain to a potential reader why s/he should read the full article. It should briefly summarise the background, the main contents and the main conclusions.
2.2. INTRODUCTION: should start with a few easy to understand statements explaining the general context of your piece of work. It should narrow down to the specific sub-area of your work, providing a motivation for this research area. It should then be followed by references to what other people have done in the field, what the advantages and shortcomings of their insights / methods etc. The reader should gain a fair overview of what is already there and why it is worthwhile to do more research and why s/he should read on.
The Introduction should close with some few sentences providing a clear and concise statement about the outline, the aims and the objectives of this work. Ideally, you should present your working hypothesis or model which you are going to verify experimentally / computationally (research report) or through a scholarly digest of the literature (essay, project module).
2.3. (MATERIALS AND) METHODS: should describe clearly which materials and methods (chemicals, kits, machinery, algorithms, web-sites, programming language, computers etc.) you have used, why you have used them, where they were taken from and what the main underlying rationale was. Lengthy lists, e.g. of web-sites, gene names etc. should go to the appendix. The description should enable anyone who is working in the field to easily reproduce this work. If you write an essay you should briefly describe literature resources and e.g. key-words you used in PubMed or SCOPUS / Web of Science for starting your investigations and how you proceed.
Reproducibility is among the key criteria to ensure scientific credibility and to avoid scathing comments from colleagues. Some clear and well commented figures may help to illustrate the methods and thus increase comprehensibility of the paper.
2.4. RESULTS: must be clearly separated and distinguishable from hypothetical statements, speculations and generalisations. The latter should be put in the "Discussion" or, if "Results and Discussion" have been put in one section into the "Conclusions" section.
Results should be described one after the other, with a clear separation between the experiments. You should unambiguously (use labels and cross-references within the text) refer to figures which illustrate the outcome.
Figures and, where necessary, tables should be clearly labelled and commented with a figure/table caption explaining precisely what is displayed and what the symbols mean. Tables and Figures should be "self-explanatory", i.e. all labels and abbreviations used in the table itself or on the figure should be explained in the caption and an informative title should be provided for the Figure (e.g. "The frequency of missing domains across clusters classified by types of annotation artifacts and real evolutionary events"). Figures should not occur before they were mentioned in the text but ideally close to where they are referred to, i.e. shortly after.
Do not report all the detailed information such as numbers in the text, try to summarise the information in a meaningful way, avoiding unnecessary details -- and put the detailed information in the tables and Figures.
Note: the Results section in an Essay is of course the part which describes and summarises knowledge and will fall together with the Discussion. This part will thus make up the major part of the whole essay. It can be followed then by a brief section "Conclusions and Outlook".
2.5. DISCUSSION: interprets the results in the context of the literature. It emphasises the significance of the work and discusses the relationship to other works (e.g. the ones laid out in the introduction) in a fair and comprehensible manner. It may close with a short paragraph comprising speculations about the wider significance of the work and an outlook to the future. Anything that is not directly supported by your own data or that have been stated by other authors should go in here (with references!).
Furthermore, you need to address possible weak points of your approach or methodology. Conclusions and outlook is optional in a report on a project but highly recommended in an essay. Here you can, based on the discussion you have done before, express an expert's evaluation of the key points and your personal opinion about future developments.
2.6. REFERENCING: *EVERY* statement based on other's work, *EVERY* piece of text written by others must be quoted, *EVERY* method (this includes programs, databases, ...) devised by others (unless already in a text-book) *MUST* be referenced appropriately, *EVERY* piece of research you build on must be acknowledged. This means that throughout the text there appear marks such as "" or "(Smith et al 1999)" when you refer to Smith's and colleagues' work. The corresponding references must be listed at the end of the article in numerical or alphabetical order respectively or in the order they have been introduced if name-tags have been used. Throughout the text you must stick to one system and the reference list must be coherent and complete. Follow either the Harvard or the Chicago system. The minimal information given in a reference is: The name of the author (if one), both authors (if not more than two), both initials of all authors, journal name (in an approved abbreviation), volume (bold or underlined):first page, year. Beware that book references include additional information like editor, book title, publisher, year and city etc. Furthermore there is a difference between citing a book in general or a specific chapter from a book.
Web-links are acceptable only if certain resources have not been published or to indicate the source of a download in addition to a proper reference but they do not count as a proper scientific source (and neither does Wikipedia).
It is recommended to use pybliographer under Linux (or whatever is available under windows if you happen to use MS products).
There is no guideline about an appropriate number of references: for a short report on a novel result some 10 (but certainly not less) might do, for a review up to a few hundred may be appropriate. Generally, as a rule of thumb, there will be between 20 and 70 in an original paper, some 5 - 20 in a short report and around 15 to 40 in an essay or project module report.
Naturally numbers for theses will be higher.
2.7. RESEARCH PLAN: (End of Project Module Report, MOGL Module for MSc and PhD 3 month literature- and 9 month transfer-report):
should contain a tabulated description of planed further research, structured as aims, objectives, tabulated lists of pieces of planned research with time estimates and required materials.
Tasks must be clearly linked to the literature and the discussions given before, i.e. it must be obvious and explicitly stated why steps are planned to be carried out, to which arguments given earlier on they are related to and why it is justified and necessary to perform each individual piece of work, why it is prioritised and which assumptions time estimates and required materials are based on.
3. Scientific Writing Style
3.0: You must always reference (see above) and never plagiarise (see below).
3.1. LANGUAGE: Keep it simple. Don't use sophisticated phrases. Stick to one word when you refer to one thing, i.e. avoid alternative expression. Use short sentences. If a sentence is longer than 25 words or two lines, try to break it down, even if the overall length of the text increases.
Avoid replacing nouns with "this" or "that" referring to object or subject of the previous sentence. Don't hesitate to reuse the same word repeatedly within a short stretch of text, simplicity is more relevant than aesthetics.
Virtually all scientific communication is in English. For year1 and year2 projects we do not force you to write in English. However, think if it would be for your own good? If you feel your English is miserably, start now to improve your skills and don't prolong your misery. You will not be penalised for improper use of language, grammatical mistakes etc.
Use spellcheckers (e.g. ispell ), thesaurus and dictionaries and check out your style.
3.2. HUMOUR: Generally, "Funny comments", silly jokes and even irony should be omitted. First of all, what you think is funny may not be fun for others. It may confuse people, occasionally irritate them or even make them feel insulted if they don't share your sense of humour. Since you do a presentation or an essay not for yourself but for the audience (and don't forget that every report you do here should be a "simulation" of a real life situation) all that counts is how people perceive your message and not how you "meant" it.
Secondly, science must always try to be as objective as possible. Considering the rather philosophical questions about choice of subjects and the contribution to ongoing debates it should be clear that in a strict sense there is no such thing as objective science anyway. So don't make it worse. Scientific reports or essays are a serious matter and should be treated as such. Some "eye-catchers", e.g. cartoons or the like are acceptable in a presentation, e.g. when you want to convey a message or illustrate a tricky point. Still: be cautious.
Finally: way too often things come awkwardly, clumsy and this is simply unprofessional.
3.3. POLITENESS AND POLITICAL CORRECTNESS: In a workshop I organised I asked one of my PhD students to chair a session with several internationally renowned scientists. When he introduced a female speaker he said "And now it is my special pleasure to introduce the first woman ...". What was wrong? Well, first of all, it should be a "female speaker" (maybe a "lady" would be acceptable too), secondly you should consider: would you (if you are male) do the same if a man speaks next?
Think along these lines whatever you write or say about members of the opposite sex, handicapped, foreigners, etc etc. ... or simply put: about other people in general !!!
3.4. PERSONAL OPINIONS AND STATEMENTS: They, too, have no place in a scientific comment. At best you can, in the discussion section, express hopes, aspirations etc. about how your results may lead all of us to a brighter future (depending on how hard you wanna beat the drum ....).
When you explain your motivation in the introduction and, at the end of the introduction, the aims and objectives of the report are laid out, you make a fairly strong personal statement anyway. That's sufficient.
3.5. EXAMPLES of poor and better style:
|Sequence 1 had 54.234% of helices, Sequence 2 had 24.2221% helices||Sequence 1 has more helical regions than sequence 2 (Tab. 1)|
|Fig. 1: Sequences 1 and 2. See text for details.||Fig. 1: Results of structure prediction for Sequences 1 (a) and 2 (b). Blue: helical regions. Red: beta sheets. Yellow: random coil. Overal structure percentage is shown on the left.|
|Since I was asked to analyse this sequence, I clicked at the NCBI web-page and made use of their nice interface. I picked the sequence our teacher gave us on a disc and pasted it in before I hit the BLAST option. I thought the parameters as set were OK.||BLAST from the online interface at the NCBI (www.ncbi.nlm.nih.gov/entrez) was used with standard settings to search potential homologs of X against TREMBL|
4.1. LENGHT: See table at the end of this document.
4.2. TITLE PAGE: For easy handling of your work we ask you to staple a cover page on top of your report. All information should be given in precisely the following manner in the top right corner of the otherwise empty sheet of paper in Times Roman 14pt:
Name: A.N. Other Course: Bioinformatics 2 Immatriculation Number: 4711 Date of submission: 29.2.2005 Word count: 4200 Supervisor: Frank N. Steen Title of essay XYZ
We ask you to submit two printed copies (single-spacing) to the yellow boxes at the general office and a pdf attachment via email to the person indicated in the course description (normally and unless otherwise indicated the supervisor in a project, the module director in a BSc or MSc advanced module or the practicals supervisor) by the deadline which is normally 12:00 of the date given as deadline (unless indicated differently on the course description). For all projects and essays except bioinformatics 2 you must also provide two CDs (for all sorts of essays such as project module, 3 month PhD report etc. one CD is sufficient) labeled with project title and your name in a simple paper sleeve which contain the following directories:
- the presentation (including the LaTeX source),
- all text as printed and supplementary material if applicable,
- progress resports,
- program sources with instructions and documentation,
- the originally used data resources,
- protocol and data files of results.
We ask you to submit two double-sided printed copies (single-spacing) and a pdf attachment via email to the person given in the course description (normally and unless otherwise indicated the supervisor in a project,
the module director in a BSc or MSc advanced module or the practicals supervisor) by the deadline which is normally 12:00 of the date given as deadline (unless indicated elsewise on the course description).
Do not use plastic covers, special binding etc. Just punch and staple your report in the left upper corner. If possible, use double-page printout ("save the trees"). You do not have to use colour printers and will not be penalised for using black and white.
5. Scholarliness and Originality
We are all standing on the shoulders of giants. There is nothing wrong about it but we must acknowledge the giants.
5.1. PLAGIARISM: You can get in serious trouble if you quote literally sentences from other authors or sources without explicitly using quotes and proper referencing. This may range from points deducted,
failing a module, financial consequences and even ex-matriculation. And this will be implemented and it is NOT A JOKE!
- using unpublished or non copyrighted sources is also plagiarism
- there are no excuses: if you copy "only a sentence" in a "less important part of the paper", without an intent to really cheat, you will still be penalised.
- modifying the text slightly or altering punctuation is not sufficient; it is still plagiarism.
- Self plagiarism is still plagiarism, e.g copying parts from a former report into a new one is also plagiarsm!
5.2. LITERATURE RESEARCH: Mining, digesting, summarising and putting into context of literature is among the most important tasks in scientific research.
Students are reminded that they must refer to appropriate resources in first place when starting any project and continue to do so in short intervals during the project.
Students must use scientific resources to accomplish a comprehensive and as close as possible to complete survey in order not to duplicate existing work and to
stay abreast with ongoing research. Best resources are SCOPUS and SCI (Web of Science) and students must familiarise themselves with forward searches
(which papers have cited a given paper since its publication) and backward searches (which papers have been cited by a given paper). As a simple example
make a search for Michael Zuker's seminal RNA algorithm and its ramifications using the query "Zuker, M." for author and "RNA" for subject. Try to answer
the following questions: which paper by Michael Zuker has been cited most frequently? Has any of the paper in which this most frequently cited paper has
been cited, been cited more often than the one by Michael Zuker? Are reviews cited more often than original articles? Which of the papers to which Michael
Zuker has referred to in his most cited paper is most highly cited (except any of his own)? Can you identify the authors and explain why? Would you consider
the paper influential and if so why? Did Zuker invent his algorithm de novo or did he build on other people's work ? (And if so, whose work ?) Read a couple
of abstracts of referred to papers in before trying to answer these questions. A further valid resource is MedLine at NCBI which is fast and easy to use but
focused on biomedical research and lacks direct links between publications. Google scholar is also useful although not very exact. Wikipedia is *not* a valid
scientific resource. It may come in handy occasionally, e.g. since pictures are public domain but any quote must be further supported by original literature.
Further guidelines (in case of conflicting information our guidelines override any instructions given in the links)
- Excellent guidelines for writing a scientific paper
- Bioinformatics: instructions for authors.
- Alverno guide to writing biology
- Writing a biology review paper
- WWU guidelines for Bsc/Msc Thesis writing
- WWU courses on scientific writing (and other stuff), and from graduate centre
6. Special Notes
6.1 For COMPUTER SCIENTISTS: Especially in Introduction and Discussion of project reports: Concentrate on the Biology! Give a scholarly and professional account of your investigations instead of your opinions,
frustrations etc. Interpret your results: what were the aims + objectives, what was accomplished, why? What could be done better next time?
6.2 A special note on ESSAYS: Essays should provide the reader with an easy to read overview on a field. Accordingly, complicated formalisms --if necessary at all-- should be supported by own(!!) graphics, schemata and comparisons between methods. This is a major marking criterion. An essay is not a report on or extract from one or few papers (which is what you probably have learnt in school) but it should provide an overview over the current state of the art of a complex and vast subject area. It should be written with a flow and may thus refer to the same work on several occasions if necessary. As a preparation to scientific work, it is important that students learn to gather, sort, select, reflect, recapitulate, digest, summarise and critically evaluate a large body of literature in a short time. A fair account of existing literature should be provided and the reader should be provided a starting point to easily delve further into the literature. In other words, the essay must be "scholarly". Essays do not contain a "Results" section in the sense that own results are described. However, the digested information should be presented in an essay to be comprehended in a novel way in order to train and prove your synthesis skills. Finally, the discussion section should provide the reader with a broader picture of the subject and some outlook that is well supported by arguments which are generated from the provided material of the study. As always, references should not be primarily to books but to current literature which is always in peer-reviewed journals. (Double check with the Bioinf 5 website). As part of the Essay, students should approach the supervisor with a sketch of the essay and list and printouts of the of materials (several weeks before submission) and a close to ready version (a few days before submission). As always, principal availability should be checked first on the group calendar and then contact established, preferably via phone. Note that it may be advisable to contact Prof. Bornberg regarding the soft skills and a group member for technical and scientific advice.
6.3 A special note on BIOINFORMATICS 2 REPORTS: These should follow the same guidelines although they are of course much shorter. The example reports on the web from earlier years were done according to other guidelines. We still ask for a short Abstract (2-4 sentences), accurate referencing, figure captions, Discussion etc. as detailed above.
6.4 A special note on the PROJECT MODULE: (preparatory module for your BSc): The report on the project module should follow the general guidelines on essays as given above but with the following differences: It should also contain a section after the discussion in which a project plan for the BSc thesis is described. This plan should contain a section on aims and objectives, expected outcome, a structured overview on work packages (if necessary with a flow chart) and a milestone planning (see for details and adapt accordingly).
6.5 A special note on THESES (BSc, MSc, PhD): Theses are not just longer than papers and essays but they should also provide some extra features. First of all, the aims and objectives section (normally the last paragraph(s) of the Introduction) should be much more elaborate and demonstrate motivation for and context of the project. It can be derived (and adapted) from the last section of your project module report (BSc), the preparatory report of your MSc (after 1-2 months) and the planning section of the 3-month literature report and 1st year transfer report if you do a PhD. Second, theses should also provide a comprehensive account of results, independently of them being successful or not. Of course not every attempt needs to be recorded and described in full detail, but the description should also provide "negative" results and a very detailed description of all methods which have been developed and/or applied, even if they were not as sucessful as one had hoped for. Theses should thus provide a solid basis for future work and help others who build on this work to avoid failures and benefit from insights on the methodology.
|length||style||1st talk||2nd talk||3rd talk|
|Bioinf 2||1000-3000 words||report - paper||none||none||none|
|Project Module||6-15 p||Essay + Research plan||within 2 weeks of report submission (marked)||none||none|
|BSc report||20-60 p||Thesis||none||recommended||1-2 weeks b4 submission (marked)|
|Proj. rep. in BSc Vertiefungsmodul||6-10 p||Paper||none||none||1 week b4 submission (marked)|
|S-Kurs, MSc FM||10-20 p||Paper||optional||none||1-2 weeks b4 submission (marked)|
|MOGL MSc||10-30 p||Essay + Res. plan||after 3 months||none||none|
|MSc thesis||40-120 p||Thesis||none||recommended||within 6 weeks after submission|
|Bi 5||3000-5000 words||Essay||none||none||submission - 2 weeks|
|PhD litr. report||10-30 p||Paper||after 3 months (marked)||none||none|
|PhD 1st year report||40-100 p||Thesis + Res. Plan||after 9 months (marked)||none||none|
|PhD thesis||70-250 p||Thesis||after 18 months (marked)||after 36 months, b4 submission||dry run|
(1) S. Becket once stated: "Ever tried. Ever failed. No matter. Try again. Fail again. Fail better." I'm not sure if this really helps. But at least it should convey the message that jumping into the cold water will,
in general, still get you faster to the goal than fickling around, thinking for ages about how to do it "best" and arguing how the goals could be redefined.
Authors: Erich Bornberg-Bauer, January Weiner