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-====== Project documentation ====== +====== Lab protocols ====== 
-===== Necessary information ===== +Most practical modules in your curriculum require that you write a lab protocol at the end of your project. This lab protocol is your proof of achievement, and thus must be taken seriously, independent of whether it is graded or not. Please find below some information that should give you an idea of what to consider when writing a protocol.
-Project documentation is essential when working in a scientific environment. Figure {{ref>docucont}} is the result of a brain storming session that tried to highlight the main information that should be provided in a project documentation. Note, this list is not necessarily exhaustive. +
  
-<figure docucont> +<WRAP important><fs 1.5em>There is a difference between a lab protocol, and the daily documentation of your work in the WIKI. You can write, in principle, a lab protocol as a set of WIKI pages, but then we expect that it adheres to the guidelines listed below</fs></WRAP> 
-{{:general:dokuwiki:docucontent.png?400|}} +===== Objective ===== 
-<caption><fs 0.8em>An unordered list of information that should find its way into a proper project documentation. +Before writing a lab protocol, you should ask yourself not only //why// your are writing a lab protocol, but much more //what you want to achieve// with the lab protocol. The answer is considerably simple: You write the lab protocol for  
-</fs></caption> +  * yourself. It should bring you in the position to easily repeat your analysis - or parts of it - somewhen in the future, and probably at a time point where you can no longer do it from the back of your head((since you have forgotten about all the details)) 
-</figure> +  * for any other person that comes after you, such that this person has a chance to understand 
 +    * what you did 
 +    * why you did it  
 +    * and how you did it 
 +<wrap important></wrap>With the help of your protocol, any person should be able to quickly reproduce your analysis. If you keep this objective in mind, then you should already have a good idea of how to write a protocol.
  
  
-===== Project report ===== +===== How to write a lab protocol ===== 
-For successfully completing the module, you will have to submit a lab protocol. As mentioned repeatedly in the course, you are encouraged to write this protocol during the course in the dokuwiki. However, please note the difference between a daily report of your work, i.e. kind of a lab book, where you chronologically note down what you did, and a lab protocol. The lab protocol is meant to give an overview of the entire project. It requires +It happens often that people have no clear idea of how to write a protocol. We have, therefore, compiled a short guideline of what to take into account when writing a protocol. 
-  * a meaningful introduction which specifies the research questions or hypotheses +  - A protocol is a scientific text, and thus the [[howto:scientific_essay|same rules]] apply 
-  * a comprehensive listing of your materials and methods that brings others in the position to reproduce your work and your findings. Make sure to not forget +  - A protocol is typically written for a short term project. Its focus is more on the technical part and the results, and less on answering a particular scientific question((It is, thus ok to keep introduction and discussion concise)) 
-    * relevant software together with their version number, their source, and the accompanying publication +  - A protocol is meant to provide<WRAP>  
-    * data sources together when they have been last accessed (e.g. databases) +    - all data 
-    * relevant parameter settings +    - all programs 
-    * list of analysed species, if necessary +    - all analysis steps 
-  * A comprehensive presentation of your results. Make sure that the reader understands what question you are currently addressing, what analyses you were performing, and what results you achieved +that are required to reproduce your analysis</WRAP> 
-  * A discussion of your results in the light of your research question. Among others, you can discuss the influence of certain filters, the limitation to a certain subset of data or taxa, your paramter settings, and the like+Follow this [[https://www.thoughtco.com/how-to-write-a-lab-report-606052|LINK]] to get some additional ideas of how to write a good report 
 + 
 +<fs 1.5em><wrap tip>It is a good idea to carefully read the guidelines {{ :general:documentation:how_to_write_scientific_text.pdf |How to write scientific text}}</wrap></fs> 
 +===== Some additional points to consider ===== 
 + 
 +Below, we have compiled a collection of points that you should check before writing a protocol, and afterwards as well 
 +==== Structure of the protocol ===== 
 +Try sticking to the standard structure<WRAP> 
 +   * Introduction 
 +   * Material & Methods 
 +   * Results 
 +   * Discussion 
 +   * References 
 +<WRAP important>Don't mix up the contents of the main sections! In particular, there is always the danger to write results in the discussion section, or vice versa! Likewise, people tend to write results into the methods section. Simply don't do it...</WRAP></WRAP> 
 + 
 +==== Figures ==== 
 +<wrap important></wrap>Before inserting a figure, think about what it should tell the reader, and then design it accordingly. In particular think about the final image size when drawing it. Figures for print are typically either 80 mm (single column) or 160 mm (two columns) wide.((it is not a good idea to draw figures in any size first and later re-scale them. This will result in font sizes and line weights that to be different for each figure!))  
 + 
 +Each figure...  
 +   * has a figure number. And figures have to be numbered in the order they are mentioned in the text 
 +   * has to be mentioned in the text 
 +   * has a short, informative title  
 +   * has a description that reflects the message of the figure. Make sure that the figure description does not end up in the main text 
 +   * should be interpretable on its own. It is generally not optimal to refer to other figures (other than supplementary figures) in the figure caption  
 + 
 +<wrap important></wrap>Watch out for the following 
 +   * Screenshots as figures can be ok, but only when the image quality is sufficiently high.  
 +   * make sure that the font and the font size is uniform across the figures. Text must be <fs 0.1 em>sufficiently</fs> large to ease the access to the figure content. 
 +   * avoid figures landscape format  
 + 
 +==== Tables ==== 
 +Like with figures, think about the information that should be provided with a table 
 +  * tables have to be successively numbered according to the order they are referred to in the text 
 +  * each table has to be mentioned in the text 
 +  * each table has an informative title. Table columns can be explained in the table footnotes 
 +  * avoid landscape tables 
 +  * avoid tables that extend over more than one page. Consider placing large tables into the supplement 
 +  * don't use vertical lines to delimit table columns. Horizontal lines to delimit rows are ok, though 
 + 
 +==== Methods ==== 
 +  * provide references for the programs you use, the URL from where you have downloaded it, and <wrap important>provide the program version together with the relevant parameter settings</wrap> 
 + 
 +==== References ==== 
 +<wrap important></wrap>Remember why we use references? This is because we have to back up each statement in a scientific text with supporting evidences. These can be either previously published **and** peer-reviewed literature, or own data. In either case, the supporting information must be invariant with time. Thus, **Wikipedia cannot serve as a reference for scientific text** for several reasons. One of the most important ones is that article contents are subject to change over time! 
 +   * Make sure that references in the text, and your bibliography is correctly and consistently formatted. We prefer the //author, year// format for in-text citations over numbers. 
 +You can read more about how to cite in this document provided by the University of Cologne (in German only): [[http://uni-koeln.de/phil-fak/storyline2/story_content/external_files/Handout_%C3%9Cberpr%C3%BCfbarkeit.pdf|Handout_Ueberpruefbarkeit]]  
 +==== Abbreviations ==== 
 +Abbreviations, that cannot safely be considered common knowledge, have to be explicitly introduced.  
 +  * For example you can write "We used the //Quest for Orthologs// (QfO) set of reference proteomes... 
 +  * Species names have to be given in full length, before you start abbreviating them. For example you should write: "(...) we extracted all ribosome biogenesis factors from yeast (//Saccharomyces cerevisiae//)". Later in the text, you can then abbreviate the species name to //S. cerevisiae//. 
 + 
 +==== Spelling ==== 
 +Most editors provide a spell checker. Make sure to use this! 
 + 
 +==== Headings ==== 
 +Headings should be concise and informative. Something like ‘Getting an idea (of) how to use HaMStR…’ should be avoided. This could be reformulated to ‘Establishing the HaMStR Workflow for …' 
 + 
 +==== Miscellaneous ====  
 +  * Use standards whenever possible 
 +  * briefly introduce relevant methods such that you - as well as any other person - comes into the position to understand what kind of analysis you are actually doing. 
 +  * Avoid lab jargon. For example, //to blast// is not the appropriate verb for //performing a Blast search// or even better for //searching for significantly similar sequences in a database using the Blast algorithm// 
 +  * Avoid group-internal abbreviations such as //DROME// as an abbreviation for //Drosophila melanogaster// 
 +  * Datensets 
 +    * Introduce data sets that you use in your analysis in the Materials section, and make sure to explain where the data is located
  
-You will find some general guidelines for writing a project report, or in general scientific text here 
-  * [[https://www.thoughtco.com/how-to-write-a-lab-report-606052|How to write a Labreport]] 
-  * How to write scientific text