MS1: overview and structure of the project required steps: WP11, WP12 responsibility: executing person time/duration: 3 - 4.5 h proof of MS1: folder-structure
WP11: brainstorming for the directory-structure for this project:
How should the workflow look like?
How many steps or folders do are necessary?
How to assure the reproducibility?
time/duration: 2 - 3 h
WP12: generation of needed directorys
Is it possible to use Git as version control system?
How to generate directorys/folders?
time/duration: 1 - 1.5 h
MS2: 50 random downloaded files of proteins required steps: WP21, WP22, WP23 responsibility: executing person time/duration: 5 - 8.5 h proof of MS2: 50 pdb-files
WP21: literature research:
What is PDB?
Structure/format of pdb-files?
Secondary structure of proteins?
time/duration: 2 - 4 h
WP22: find possibility to download the files:
What is Biopython?
Can Biopython download the table of contents from PDB?
time/duration: 2 - 3 h
WP23: selection of the dataset:
How to select randomly the 50 pdb-files?
How to save the files?
time/duration: 1 - 1.5 h
MS3: table with the frequencies of amino-acids in proteins relative to the possible structures required steps: WP31, WP32, WP33 responsibility: executing person time/duration: 2.5 - 4.5 h proof of MS3: csv-file
WP31: literature research:
Possible amino-acids in proteins?
Characteristics of amino-acids?
time/duration: 1 - 1.5 h
WP32: calculation of frequencies:
How to calculate the relative frequencies?
Are there formulas available which are working?
time/duration: 1 - 2 h
WP33: generation of a logical/readable table:
How to summarize the results in a good overview?
How should the table look like?
Which file-format is necessary to save the table?
time/duration: 0.5 - 1 h
MS4: visualisation of the table of MS3 required steps: WP41, WP42 responsibility: executing person time/duration: 2 - 5 h proof of MS4: plot
WP41: literature research:
Is it possible to plot it with Biopython?
time/duration: 1 - 2 h
WP42: generation of a plot:
How to generate a self-explanatory plot?
How to label the axis and legends?
How to save the plot?
time/duration: 1 - 3 h
MS5: validation of the results required steps: WP51, WP52 responsibility: executing person time/duration: 3.5 - 4.5 h proof of MS5: approval of the results
WP51: control of the workflow of the project:
Was each step performed without errors?
Was the execution of MS1 - MS4 possible?
Was the execution of MS1 - MS4 exact?
time/duration: 0.5 - 1.5 h
WP52: control of the results:
Are the results plausible?
Which amino-acids usually lead to alpha-helix or beta-sheet?
Which literature and databases could be taken for comparison?
time/duration: 3 - 4 h
MS6: close of the project required steps: WP61, WP62 responsibility: executing person time/duration: 2.5 - 6 h proof of MS6: report/presentation of the project
WP61: control if MS5 is finished:
Is the approval of the results available?
time/duration: 0.5 - 1 h
WP62: writing a report or/and presentation:
How to summarize the results of the whole project?
How to interpret the results?
How to write in an understandable form?
time/duration: 2 - 5 h