Some years ago, I presented a retrospective of the graph drawing (and related)experiments I had conducted since 1995 to an audience of information visualisationresearchers, describing the process I went through in defining a newexperimental research area and learning to run human–computer interactionexperiments. This was an honest and reflective seminar in which I highlightedthe mistakes I had made, the good and bad decisions, and how my knowledgeof experimental design had increased and improved with every experiment. Atthe end of my presentation, a member of the audience asked, “So, Helen, whatis the ‘Black Art’? What is it that you have learned about running experimentsthat we should all know?”

This started me thinking about how much expertise is embodied in experienceand seldom communicated apart from in a master/apprentice model.PhD supervisors can advise students on how to formulate and conduct experiments,psychology and HCI research texts can be read, and other experimentsin the research literature can be copied, but the actual step-by-step process ofdesigning and running an experiment is rarely written down and communicatedwidely. Although I believe that one can never understand the process of conductingexperiments without experiencing the process oneself, I also believethat experiences can (and should) be shared and that advice resulting fromothers’ experiences can always be useful.

So, now you have your results, and you want to tell everyone about them. This chapter discusses the way in which you report your research, typically in a research article for an academic conference or journal, or in a dissertation for assessment. In all cases, you need to keep in mind that someone else will be reading what you write, and that this person has not been party to your decision-making process. It is easy to leave information out because it appears obvious.

Reviewers’ concerns

It is the job of reviewers or assessors to make a judgement on the worth of your research, and it is your job to make sure that you have presented it sufficiently well that they can do so. This is true of all research; however, writing experimental papers brings with it its own particular issues:

• An experiment focuses on addressing specific research questions: reviewers may not believe that these questions are interesting or important.

• An experimental research question could be addressed in many different ways: everyone will have their own idea as to how best to address it.

• Different statistical methods are favoured by different people: beware the reviewers who are well versed in statistics when you have not analysed your data using their favoured method!

• No experiment can ever be perfect: reviewers can easily find faults on which to base a negative judgement if they want.

• Many reviewers have never actually designed and conducted an experiment themselves: they do not always appreciate the amount of work required for running experiments, the difficulty in making appropriate design decisions, or the constraints that apply to experimental design.

So far, we have assumed that everything will go smoothly; however, in practise, this is rarely the case. All will not go as planned, especially if this is your first experiment. Thus, this chapter discusses some of the things that can go wrong, and gives suggestions as to how to prevent them occurring, or how to deal with them if they do. Problems can be prepared for, and in many cases, following the advice given in this and previous chapters will put you in a good position to address them (be forewarned!). Pitfalls are those events for which you cannot prepare but that must be dealt with in order to rescue the situation.

Problems

Pilot tests show that the experimental design is fundamentally flawed. You may have put a great deal of work into preparing the experimental objects, tutorials, etc., only to discover that the task given to the participants is simply too difficult and takes too long, that the participants cannot understand what is expected of them, or that the tasks are actually inappropriate for the different conditions. The concept of pre-pilots (and even pre-pre-pilots!) is useful here. Piloting is an iterative process. Although you must pilot at least once with the full experimental method before running it, it is useful to run smaller, partial pilots on some aspects of the experiment before putting it all together. For example, get feedback on the tutorial from a colleague to find out whether it is clear, or ask someone to perform the tasks on the experimental objects on paper to determine whether they are appropriate. By the time you get to running the final pilots, many of the potential problems will have already been addressed.

Where you will become BFF with GFF

The average life scientist will spend a lot of time working with data. Increasingly, this data will exist in the form of large data sets that will have been downloaded or extracted from one of the many large biological databases that are accessible on the internet. Such in silico data might consist of a small number of very large files, a large number of very small files, or anything in between these extremes. However, in many cases the default file format for those files will be plain text. The actual format of the plain-text file will vary a lot, but the fact that it is plain text means there are many Unix commands that are just waiting to get their hands on your data.

This part of the book will cover a small number of extremely powerful Unix commands that are well suited for slicing and dicing text files. If you are reading this part of the book after working through the ‘Essential Perl’ section then you will spot the similarities between some of these commands and some of the operators in Perl. Conversely, if you have yet to start learning Perl, you will find this section introduces many topics that will be revisited as you learn Perl.

Introduction

In the previous chapter we discussed analysing and interpreting the assignment topic and compiling a work plan. In this chapter we will learn how to search for and find relevant information so we can write an appropriate and relevant assignment answer. We are going to look at what information we need to retrieve; where we will find this information; how we will retrieve the information; and how we know which retrieved information is best for our task.

The keywords, headings and subheadings on the work plan are a good place to start. They indicate what information we need but now we need to consider where we will find this information.

What does retrieving information involve?

Retrieving information involves two steps:

1. 1. Locating relevant sources

2. 2. Selecting the information

These two steps involve several activities. To retrieve information we need to locate sources in a collection either by physically going to the library or accessing sources via the Internet and then selecting relevant information from these sources. Relevant information is information that directly applies to the assignment topic. For example, look at the following assignment question:

Relevant information has a direct relationship to the keywords and headings which we have jotted down on the work plan. We identified the keywords as Internet search engine; Google; Yahoo; evaluate website. Also on our work plan we jotted down various subheadings under the main headings. (Refer back to the work plan in Chapter 8 for these headings.)

When we start looking for information it is generally easiest to turn to our own collection of books and periodicals. However, our own collection of books and sources are generally not extensive and will therefore not give us enough relevant information for completing an assignment. An external collection, such as a library, on the other hand, contains so many different information sources that our search for information will be more complicated. Either way, the steps involved in searching for information are the same, whether they relate to an internal or an external collection. The steps are just simpler when the collection is small and when we are familiar with using it.

Introduction

In the previous chapters we have already focused on many of the prewriting activities necessary for writing an essay assignment. We have discussed the work plan and taking notes; evaluation of your information and ensuring your information is relevant to the topic. In this chapter and the next chapter we are going to focus on the main activities involved in the actual writing process including the prewriting activities, drafting, rewriting, organisation and structure, final editing and proofreading. We hope by giving you some pointers and showing the various techniques you will be better equipped to face this task and feel less anxious about writing an essay assignment.

Writing is not an easy process even for experienced writers. To write well you constantly need to reshape, refine, and rewrite. Inexperienced writers often write poorly because they do not realise that writing is not a linear process but requires constant reworking and revision of their initial ideas. In other words it is an iterative process.

Prewriting

Prewriting activities are the processes you go through before you even begin writing. Prewriting activities give us a better idea of what we want to communicate, how we are going to say it and why we want to communicate it to a reader. In writing you need to first identify your audience and your purpose. These are both important prewriting activities that you need to do before you can begin writing.

Some of the important questions you need to ask yourself before beginning are:

• • Who are your readers?

• • What do they expect?

• • What do they know about the subject?

• • What special terms or concepts might you use that will have to be explained to your readers?

• • What is the purpose of your writing?

Time spent in prewriting activities will not be wasted because these help you to make sure that you answer the assignment question, and are aware of your purpose and audience.

Lecturer as an audience

When you write an academic assignment it is a particular situation with particular requirements that have to be met. Although you know that the lecturer reading and evaluating your assignments is knowledgeable about the topic, you have to write as if he or she knows nothing about the topic.

Introduction

Read the following scenario and then answer the questions below:

If we look at the scenario above we can see that Veli had problems with her assignment because she wanted to start writing as soon as possible. She skipped the interpretation and planning stage and began immediately looking for information. As a result she read sources and took notes without a clear idea of what was relevant. All she had was a very general idea of the topic. Then when she sat down to write the assignment she found that some of her notes were irrelevant and she did not have enough information on some of the important aspects of the topic. She also found that her marks did not reflect the amount of work that she had put into the assignment. This could have been avoided by spending some time interpreting the topic.

• • Do you take time to read and analyse an assignment question? Yes/No

• • When you start working on an assignment do you have a work plan? Yes/ No

• • Do you identify the keywords in the assignment topic before you begin finding information? Yes/No

If you answered no to these questions then it is very important for you to study this chapter because in this chapter we will learn how to analyse an assignment topic and develop a work plan.