Tips and hints on how to prepare and write a diploma/BSc/MSc thesis

version 18 October 2005

(-> an updated version focussing on scientific writing style and the theis manuscript components 10 Aug 2010 is available for download as a pdf. )

Introduction

What is the purpose of a Diploma thesis?
***Note that all the following in general equally applies to BSc and MSc theses***

A Diploma thesis is your first ability to show how well you can independently (1) put your work in a wider, interesting and exciting context, (2) plan and (3) carry out a scientific study, (3) analyse and (4) represent data critically and (5) interpret your work critically while highlighting its main contributions to the field. Try to be original. Show your enthusiasm.

Despite Do not hesitate to be yourself – within the expectations formulated above.

The skills you need to develop for a good diploma thesis are manifold: good overview of the literature, good planning, hard and effective working in the face of a deadline, good data analysis abilities, good writing qualities, a feeling for nice lay-out, endurance and a proper degree of perfectionism.

Nobody is perfect. Everybody is different. Hence, know your personal skills: the good ones and the ones that can be improved. Don’t bask too much in the first ones. Never stop working on the latter.

English or German

There is no requirement or expectation that your diploma thesis should be written in English.
Writing in English offers you the advantage that you practice your written English, which is an advantage when going on for a Ph.D. It also facilitates giving presentations during scientific conferences.If you write your diploma thesis in English, you may have an “application advantage” when applying for a job in a private company or for a Ph.D. position elsewhere (e.g. Max-Planck or abroad).
A main disadvantage is that when your writing skills in English are poor, you may not be able to produce a text that reads as nicely and fluently as what you would be able to present in German. Although a diploma thesis is not a language test, your marks may be lower when writing in English than in German simply because your writing sounds not very scientific or even awkward and funny.
When writing in English (a foreign language for most of us) consider that this takes much more time, probably two times or more! Consider this!

Time

A diploma thesis lasts 9 months. You will spend this time with various activities, such as reading literature, developing concepts, planning experiments (e.g. writing detailed work protocols, if you use molecular methods), running experiments, data analysis, writing up, etc.. As a rule of thumb, try to allocate one third of your available time to each of these three sets of activities:

• reading, developing ideas, planning experiments, refining experiments
• lab work
• data analysis and writing down

Especially the first set is often badly neglected in favour of the second one. Consequently, many people waste their time, running many trial-and-error experiments.
Plan more time than what you intuitively think you might need. Make sure you have extra time for distraction and relaxation (e.g. frisbee game).
Do not plan to go beyond 9 months. Although the deadline for submission can be shifted, this is only done when the reasons are beyond the responsibility of the candidate (e.g. an experiment failed and had to be repeated). Slow progress with writing or analysing your data is not necessarily a good reason for postponing submission.
Set your own deadlines always well before the ones imposed by others. E.g. plan to have everything finished 2 weeks before the official submission date. This gives you “quality time” to make your work even more perfect.
The intellectual part of your work has a higher value than the practical part. Collecting data is easy. Designing a proper experiment that fits in a wide framework and discussing the results critically, in a context, is the hard part. Hence, do not spend more time on more data. Spend more time on reading, thinking, writing and clear presentation style.

Evalutation

Quality has nothing to do with statistical significance or length!
Writing up is at least as important as the data itself. If your work was carried out and written up properly, you will get good marks – irrespective of whether your results were significant or not. If you did the practical work in the lab in an excellent way – but the context of your work is unclear and your thesis badly written – you will get poor marks.
An optimal size for a Diploma Thesis is 40-80 pages. If you need more, you probably write too extensively. If you need less, you probably have a poor introduction and discussion!
Analysing your data and writing up your thesis

Start reading the day you know what you want to do for your thesis. Read for one or two months while planning your work. A lot of reading at the beginning will give you more confidence, better guidance and more interesting results.

Start writing the “introduction” and “experimental design” even before you start the practical work.
Do not stop reading while carrying out your experiments or analysing the data. The extent to which you “know” your literature is a very important part of the quality of your work.
Build up a database with the relevant literature. Relevant does not mean all literature. Pick the highlights – the papers in the better journals. Have the best representations for certain opinions, statements, hypotheses or data. If in doubt which paper to take, take the most recent one, or cite both.
Get familiar with the program ENDNOTE and use it to organize your growing literature database. Endnotes "search functions" will help you to quickly find relevant papers when you need them. Even more important, a well kept ENDNOTE file will save you a lot of time when you write down your thesis (citing references in text and automatically creating the “References”-section of your thesis).
After data collection, spend a lot of time to carefully enter and check your data. A lot of time can be saved when entering the data in such a way that they can be analysed conveniently. Many tips are giving during the statistical course (also online). Your supervisor is glad to give you some advice. Every study is different in this respect and some knowledge of statistics is required before you start entering your data. Much time is waster by people who enter their data in ways that cannot be analysed statistically.

Use different software packages to process your data:

• Excel: For storing and organizing (e.g. sorting) your raw data. (Be sure to always keep one sheet with the untouched raw data, just in case you mess something up!)
• SPSS: for most statistical tests.
• Sigmaplot: for creating graphs

Note: Each of these programs can (in theory) be used for everything, however every single one is the best at its “speciality”. Never ever - try to create serious (i.e. to be used in publications) graphs with Excel
Use SPSS or JMP. Use Excel to organize and process your raw data, but do not use it for other purposes (statistics, creating graphs) . It is far too cumbersome for other purposes Get familiar with SIGMAplot and use it for creating graphs. It is much better than any Statistics program to change the appearance of graphs. The initial time investment by learning these programs pays off quickly.

Always start with a quick (!), preliminary, descriptive data analysis. Check for trends.

Do the final statistical analyses while writing the results section of your thesis. This helps you to make sure that you do all the analyses you need, and no analyses that you do not need. Many students analyse far too much. Do the strictly necessary analyses. The more you calculate statistics, the more likely it is that you draw wrong conclusions (always remember what really P means).

When lost during the analysis, go back to your main goals. If you have defined them properly, it is easy to separate the core essentials from the noisy decoration.

Contents of your thesis

Before you start to write down your thesis

Outline the complete thesis in paragraphs (e.g. Introduction, 1^st paragraph, 2^nd paragraph, etc.; Methods 1^st paragraph, 2^nd paragraph, etc.) in a “structure document”. Write down one short(!) sentence which summarizes the content of each paragraph. Do so for your complete diploma thesis. This is the main structure of your thesis, and the basis from which you do ALL further writing. Check with your supervisor if he likes the structure. During writing you may find out that you want to add paragraphs or delete others. No problem. Just change it in your structure document

Advantages:

• You dont waste time writing many pages on things that your supervisor does not like.
• You have a better picture of what remains to be done.
• You avoid redundancies within the main parts of the document (i.e. Intro, M&M, Results, Discussion).
• You dont loose the “big picture”.

 

Abstract

Never forget that the abstract is often the only thing readers will read from your thesis. Pay attention to it! Make it very concise, clear-cut, easy to read. Avoid technical terms or complicated reasoning.
First 1-2 sentences: introduction to the concept.
Next 1-2 sentences: the system and the specific question.

No methods, unless unavoidable or new.

Next x sentences, a brief summary of the results.

Final 1-2 sentences: conclusion.

You can end with a sentence that hints at the major topic of the discussion. For instance: “We discuss the relevance of these results for the evolution of low-altitude flying in Dumbo’s and other anti-gravitational objects.”

Introduction

Themes (to be addressed in this sequence, and each about half a manuscript page long!)

The general framework. VERY GENERAL

The (more) specific question

The system under investigation (essentials)

The working hypothesis

How this hypothesis will be tested VERY SPECIFIC

Do not

try to review all the literature (unless you are writing a review). Only mention the most relevant papers.

mention exceptions unless their relevance to the central scope of the paper is clear.

talk about problems that are not directly related to the data.

mention any of the results of this manuscript.

refer too much to unpublished material (minimise it).

Methods

The following sequence is advised

More details on the animal system

Collection sites

Culture conditions

Experimental procedure(s)

Statistical procedures (very brief, unless special)

Be accurate! It must be possible for readers to reconstruct the complete experimental procedure. It is possible to refer to other papers for standard techniques. But at least summarize them briefly when you think they might not be commonly known.

Make sure that you include only those data sets that are relevant to your main topic. Cluttering your paper with all the data sets you have must be avoided when there are many, heterogeneous sources. Showing a few convincing data sets is the only good solution.

Explain why you collected different data sets.

Descriptive data that do not contribute to the main topic of the manuscript, but that are needed to show what material was available for the “main” analysis, may be added to the methods.

Results

Be extremely concise and stick to a subdivision that relates directly to what you “promised” your audience in the introduction.

Only describe and interpret your data objectively. Do not speculate, that is part of the discussion.

Do not describe in detail those data that are already presented in tables or graphs. Summaries tables and graphs instead and point out overall effects and trends.

Do not present exactly the same data once as table and once as figure

When describing a result use the following order: 1. result, 2. statistics (e.g. "Female frogs were significantly larger than males (two-tailed t-test, t=6.72, P<0.05)".).

When mentioning statistics, always mention FOUR elements in the following order (i) the test used (ii) the statistic-value (e.g. F or t value) (iii) the degrees of freedom and (iv) the probability of the statistic for the df.

Round numbers to 2-3 significant digits.

Move statistics to the legends of tables and figures if possible. Limit stats in the text. DO NOT repeat statistics in text AND legends.

Average ± SD is preferred over average ± SE. Why?

When P = 0.000, write P < 0.001.

Avoid bibliographic references in the Results section.

Use Italics (Kursiv) for statistical variables (F, t, P, etc.)

Discussion

Start out by summarising your results in a few sentences.

Then link your results to the “hypotheses” formulated in the introduction and point out any similarities or differences from what you had expected originally.

Carefully consider and discuss possible alternative explanations for your results.

You can further speculate about any of your results, but be careful not to “take off” in daydreaming.

It is good to end with a paragraph discussing the possible problems in this study and making suggestions for future studies.

End with a “Conclusion” paragraph, which once more briefly summarizes what the main outcomes of your study are.

Acknowledgements

Your choice. Usually all the people who commented on the ms are acknowledged, as well as the technical assistance etc. who cooperated. Do not forget to mention funding agencies (e.g. the DFG) when your project was supported by external sources.

References

Limit yourself to the most relevant references.

Make sure that all the references mentioned in the text are also here, and that this list does not contain references not mentioned in the text (double cross-check!).

Use the program "Endnote".

Tables

Always put one table on one separate page for scientific manuscripts.

Are you sure you cannot represent your data graphically? A graph is much better in transferring a message than a table.

Write a good, clear legend that can be understood without having to read anything else!

Clear, open layout. Nowadays, a lot of journals only use horizontal lines in tables.
No vertical lines are used to separate columns.

Reduce the information in the table as much as possible. If it becomes too long, consider moving some of the statistics to the legend, or split one table in two.

If you repeat something in each data cell (e.g. % or cm), move it to the label at the top of the column. Keep data cells as “empty” as possible. Only the unique value that belongs there, should appear.

Word has a lot of wonderful ways of creating nice tables.

Figures

Write a good legend (see tables).

Take into account that figures are usually printed in a small size. Hence, select large fonts for labels and titles or make the graph small. Do not use very thin hairlines: they may become invisible after reduction.

Axis-titles have to be brief, but complete. Look for the briefest (meaningful) expression you can think of. Always mention units (between brackets).

Select axis-ranges in such a way that not too much empty space is left. Log transform where useful.

Select very distinct patterns or levels of grey (e.g. black an white) to distinguish between subgroups in the graph. Patterns (hatched or cross-hatched) are better than shades. The latter may become smeared after reduction and reproduction. It is nice to use colour – but consider how your graph looks like when copied!

Always use the same standard pattern and colour for the same subgroups throughout the text (e.g. white for females, black for males).

Typing style

Formating: When you start writing down, DO NOT get lost with the many formating possibilities in Word. Concentrate on the contents, not the form. Assign the following formats to your text:

Use "Standard" for the main text body. Everywhere. No exception.

Use "Überschrift1" in the lines that define the main document strucure (i.e. Abstract, introduction, Material and Methods, etc.)

Use "Überschrift2" and "Überschrift3" for the substructure of the document within these parts.

Use another format (e.g. "StandardWeb") for the legends of your graphs and tables. This allows you to use a slightly different font (e.g. 11point) than in the main text body.

Don't play around with the many styles and fonts during writing! If you format your document in the above way, you can change everything in a snapshot at the end. With a few mouseclicks you can try all the styles you like AND with two additional mouseclicks, you can automatically create an index of the whole document But restrict such activities to the very end of the writing process.

Do not forget to add page numbers. A manuscript sometimes may have to be reassembled (e.g. when your supervisor drops it when falling asleep in the train …).

Headers (Kopfzeile) and footers (Fußzeile) are not necessary, but may help to make orientation easier. If headers and footers vary from one section to the next, subdivide your text in “sections” by adding section breaks. This allows you to define a separate style for each section. It is also useful to add a large table on a “landscape” oriented page in-between “portrait” pages.

Standard style is: never a space before, but always exactly one space after ; , . : ? ) } ]. This prevents “lonely” commas or periods to move to the next line. That looks silly.

For the same reason, never a space after, but always one space before brackets: ( [ {

Always put exactly one space before and after < > = etc.

Keep things you want to be kept together in one block by separating them by a “non-breaking space” (Ctrl-Shift-Space). E.g. C. elegans looks funny if the C. and elegans are on different lines. With a non-breaking space, they always stay together. Non-breaking hyphens also exist (Ctrl-Shift-Hyphen).

Avoid writing text in brackets as much as possible.

Titles: Do not number major (sub)titles. Number paragraphs only if really necessary. It is often a good idea to use similar subtitles in the introduction, methods, results and discussion. This makes it easier to see the link between the 4 main parts of the manuscript.

It used to be commonplace to underline text that is supposed to be printed in italics (e.g. species names). At the moment, more and more journals request the manuscript as an electronic file. If so, it is best to write in italics and not underline (see instructions to authors).

Do not use boldface or italics for references in the text.

Write references in the text consistently in the same format. Separate authors by semicolon. Check with the target journal for the format to use. For instance:

(Baur & Chen 1990, 1992; Leonard 1994)

(Baur and Chen, 1990, 1992; Leonard, 1994)

(BAUR & CHEN 1990, 1992; LEONARD 1994)

“et al.“ is used for references with more than 2 authors and replaces all authors but the first. Some journals require you to write all authors when there are 3 and when they are mentioned for the first time.

The normal sequence is: oldest first. For more references of exactly the same authors in the same order: write authors once and add successive years of publication

Remember: All this can be done automatically with Endnote.

Be concise: Eliminate ALL superfluous words and expressions. Shorten sentences when possible. Cut long sentences in short ones. Be aware of possible ambiguities.

Be fluent. Connect sentences in a “logical, intuitive” manner by using e.g. “therefore”, “on the one hand … on the other hand ...”, “however”, “(al)though”, “yet”, “despite”, “whereas”, “consequently”, “as a result ...” … but use them correctly!

Use a spell-checker, but realise that spell-checkers are stupid because they do not recognise a typing error when the result is an existing word (e.g. women and woman). Grammar checkers can give some useful advice too, so use them – but think, too.

Be consistent in the use of scientific expressions. Don't use different expressions for the same thing.

Spelling is learned best if you use a dictionary frequently. But be careful! For non-native English speaking people, dictionaries are often a source of “wrong” words resulting in funny expressions. Use online dictionaries to check all the meanings of rare words. Sometimes a word has a funny meaning you are not aware of ...

Do not use “julian date” (days since 1 January) in a manuscript, use the real date instead. Only in data files it makes sense to use the julian date because of calculations and graphical representations.

Always write years in full: 1994, not 94.

Think about the date format: December 6, 1996 is US style. 6 December 1996 is British style. Months are often abbreviated to the first 3 characters (Jan Feb Mar …).

Other commonly used abbreviations are: days = d, hours = h, liters = l, molar = M, …

Do not use abbreviations such as “I’ve done this every breeding season” or “It’s a female” or “can’t”. Correct are: “I have”, “It is” and “cannot”.

Use line spacing 1.5 or 2. Assign this spacing to your "Standard" (used for the main text body) by using the option "Format ändern" (DO NOT make any changes for individual paragraphs).

Some final hints

Be safe!

SAFE YOUR DATA AND TEXT EVERY DAY ON DIFFERENT DISKS

Renumber your files, and keep the older versions. Sometimes you want to return to older versions. E.g. MyDiplom01.doc, MyDimplom02.doc, MyDimplom03.doc.

Printing frustration

Avoid trouble when printing

• by defining the printer that you will use as the default printer on your computer. This assures that the lay-out on the screen is identical with what you shall print. Often, texts are printed on another computer as where they were written. If the default printer differs – your lay-out may differ too – and the text may be shifted.
• by adding page numbers immediately: Print-outs that get mixed up during breakfast can be reassembled quicker.
• by making sure that an extra toner cartridge and paper are around.
• by putting graphs and their legend in one frame. This way, they are not separated when moved between pages.