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12:34, 5 September 2025 WikiSysop talk contribs created page File:Consensus.png
12:34, 5 September 2025 WikiSysop talk contribs uploaded File:Consensus.png
11:05, 5 September 2025 WikiSysop talk contribs created page File:Correlation.png
11:05, 5 September 2025 WikiSysop talk contribs uploaded File:Correlation.png
11:05, 5 September 2025 WikiSysop talk contribs created page File:Alfabeta.png
11:05, 5 September 2025 WikiSysop talk contribs uploaded File:Alfabeta.png
11:04, 5 September 2025 WikiSysop talk contribs created page File:Calc.png
11:04, 5 September 2025 WikiSysop talk contribs uploaded File:Calc.png
14:03, 3 September 2025 WikiSysop talk contribs created page Example code - Regex (Created page with "__NOTOC__ == Files used in example == [http://teaching.healthtech.dtu.dk/material/22116/people.db Database (text file) of people] == Average height of certain people == In the file there are entries like <pre> CPR: 230226-9781 First name: Anton Last name: Gade Height: 201 Weight: 65 Eye color: Black Blood type: A+ Children: 081154-2786 120853-1151 050354-4664 </pre> The problem we want to solve is to find the average height of the people in the file with a user given fi...")
14:01, 3 September 2025 WikiSysop talk contribs created page Regular expressions (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Dict techniques |Next: Python object model |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_12-Regex.ppt Regular expressions in Python]  Video: [h...")
13:30, 3 September 2025 WikiSysop talk contribs created page Example code - Dicts (Created page with "__NOTOC__ == Files used in example == [https://teaching.healthtech.dtu.dk/material/22116/apachewiki.log Log from web server] == Web server statistics == It is of interest to the BOSS to see how many visitors a web site has and how many web pages has been seen. So therefore someone (you) has to make some statistics from the web server log file. == Example of a log entry == This is one line split in 3, so it can be seen. 52d3ccde.dynamic-ip.k...")
13:28, 3 September 2025 WikiSysop talk contribs created page Dict techniques (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Set techniques |Next: Regular expressions |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_11-Dicts.ppt Dictionaries] <!-- Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=61d288cc-5f62-4027-a83e-af27012c27d2 Dictionaries] Video: [https://panopto.dtu.dk/Panopto/Pages/...")
09:07, 1 September 2025 WikiSysop talk contribs created page Example code - Wrong parsing (Created page with "Sometimes people think that when they need to parse a SwissProt file or a Genbank file (or even a fasta file), they need to separate the file in entries. While that is not completely wrong - you do need to keep the entries apart from each other - then the way they go about it is wrong. Here is what typically happens. <pre> # Read the file with open('swissprotfile, 'r') as infile: content = infile.read() # Now the file is read into content every byte of it. # That mea...")
21:41, 31 August 2025 WikiSysop talk contribs created page Set techniques (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Simple Pattern Matching |Next: Dictionaries |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_12-Sets.ppt Sets] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=e69a7b62-4f83-4b92-b254-af27012c464e Sets] == Subjects covered == * Sets, which are unordered data collections with no dupli...")
15:47, 29 August 2025 WikiSysop talk contribs created page Simple pattern matching (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Functions |Next: Sets |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_11-PatternMatch.ppt Pattern Matching] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4a8a478b-33e4-4a7a-bc38-af27012cf23f Pattern matching in Python] == Subjects covered == String pattern matching, stripping, re...")
15:26, 29 August 2025 WikiSysop talk contribs created page File:StandardDeviation.gif
15:26, 29 August 2025 WikiSysop talk contribs uploaded File:StandardDeviation.gif
23:43, 28 August 2025 WikiSysop talk contribs created page Example code - Lists (Created page with "== Analysing string content == This is an upgrade of the previous "Determine the input". Here every word, integer and float on the line is counted. Quite a few list concepts are used - on purpose. <pre> inputstring = input("Enter something and I will figure out what it is: ") inlist = inputstring.split() # ints, floats and words count resultlist = [0, 0, 0] resultname = ('ints', 'floats', 'words') # Analyze for item in inlist: try: itempos = 2 result...")
13:43, 27 August 2025 WikiSysop talk contribs created page File:BullsEye.png
13:43, 27 August 2025 WikiSysop talk contribs uploaded File:BullsEye.png
13:37, 27 August 2025 WikiSysop talk contribs created page Example code - Functions (Created page with "__NOTOC__ == File used in example == [http://teaching.healthtech.dtu.dk/material/22116/aln7.fsa aln7.fsa] == Finding consensus sequence from protein alignment == This simple consensus sequence finder simply looks at each position on all the sequences in an alignment and picks the most frequent occurring amino acid as the consensus for that position. In case of tie, the first one according to the sorting algorithm is chosen. Stupid and random, but a good practical example...")
13:33, 27 August 2025 WikiSysop talk contribs created page List manipulation (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Stateful parsing |Next: Functions |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_7-Lists.ppt Lists and Sequences] <!-- Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=871af158-9477-47c6-8e89-af27012d6e8d The basics of lists in python] Video: [https://panopto.dtu.dk...")
11:36, 26 August 2025 WikiSysop talk contribs created page Functions (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Regular Expressions |Next: Advanced Data Structures and New Data Types |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_04-Functions.ppt Making functions] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=f509116f-48e5-445b-bf6e-af27012ba23f Functions in Python] Monday ...")
11:19, 26 August 2025 WikiSysop talk contribs created page Stateful parsing (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Exceptions and Bug Handling |Next: Lists |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_08-StatefulParsing.ppt Stateful Parsing] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fe50507e-9009-49b1-a3a8-af27012d8cdf Stateful Parsing] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewe...")
11:14, 26 August 2025 WikiSysop talk contribs created page Example code - Exceptions (Created page with "== Determining input type == How to determine the input with try/expect. This is not really how it is done in practice, but it is still good to understand the ideas, because sooner or later you run into a situation where parts of this is useful. <pre> inputstring = input("Enter something and I will guess what it is: ") try: # This assignment will succeed mytype = 'string' # This may fail, in such case our exception handler is called result = float(inputst...")
11:14, 26 August 2025 WikiSysop talk contribs created page Exceptions and bug handling (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: String manipulation |Next: Stateful parsing |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_05-Exceptions.ppt Exceptions and bug handling] <!-- Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=d230fcd7-c06c-414e-a14d-af27012e22f6 Exceptions] Video: [https://panopto.dtu.dk/Panopto/Pag...")
11:07, 26 August 2025 WikiSysop talk contribs created page Example code - Changing tabs to spaces (Created page with "== Replacing tabs with spaces == As you may have discovered by now, Python is very sensitive about mixing tabs and spaces in the indentation. This program discovers all the tabs and makes them into spaces. You can decide how many spaces a tab should be. The program is meant to work in a Unix environment, and Jupyter Notebook will tend to make it superfluous. <pre> filename = input("Filename: ") spaceno = int(input("Number of spaces instead of a tab: ")) # Make a st...")
11:04, 26 August 2025 WikiSysop talk contribs created page String manipulation (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Pseudocode and comments |Next: Exceptions and bug handling |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_04-String.ppt String manipulation] Resource: Biological knowledge needed in the course Resource: Example code - Input Output Resource: [https://teaching.healthtech.dtu.dk/mater...")
08:56, 26 August 2025 WikiSysop talk contribs created page Collection of files (Created page with "__NOTOC__ Last updated: September 1, 2025 Warning: This is not complete or correct yet. == Files used in various exercises == To download the files to your system, just press the Shift key while you left click on the blue link. Follow the instructions. You can play around with these files as much as you like. If you change or destroy them, just download them again. Put the files in your course folder on your computer. <!--The files have been zipped togeth...")
17:36, 25 August 2025 WikiSysop talk contribs created page Pseudocode and comments (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: The path and simple file reading |Next: Python Input-Output |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_03-PseudoComments.ppt Pseudocode, comments and user interface] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=79ac24c4-603c-4a6e-9343-af2701292c8c The use of pseudocode and comme...")
16:49, 25 August 2025 WikiSysop talk contribs created page Example code - File Reading (Created page with "== Numbering and printing a chunk of file == <pre> print("Numbers and prints a section of a file.") filename = input("Filename: ") fromline = int(input("From line: ")) toline = int(input("To line: ")) with open(filename, "r") as infile: # keep track of the line number linenumber = 0 # iterate over the lines in the file for line in infile: linenumber += 1 # went past the required last line if linenumber > toline: pas...")
16:49, 25 August 2025 WikiSysop talk contribs created page The path and simple file reading (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Python Recap |Next: Pseudocode and Comments |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_02-PathFile.ppt The path & simple file reading] Resource: Example code - File Reading == Subjects covered == ''with'' statement, just a simple use of it. ''open'' function for opening files for...")
15:05, 25 August 2025 WikiSysop talk contribs created page Example code - Basics (Created page with "== Decimal to Binary number converter == I am a bit unhappy about this example due to the required knowledge of binary numbers, but as such the example is great. Youtube: [https://www.youtube.com/watch?v=2SUvWfNJSsM Binary numbers - watch from 2:00 to 6:00] [https://en.wikipedia.org/wiki/Binary_number#Representation Wikipedia on binary numbers] <pre> print("This script converts whole numbers (integers) into binary.") # Ask for user input number = int(input("Ente...")
15:03, 25 August 2025 WikiSysop talk contribs created page Python recap (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Programme |Next: Simple File Reading |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_01-Recap.ppt Python Recap] Resource: Example code - Basics  == Subjects covered == Variables (nu...")
15:37, 4 August 2025 WikiSysop talk contribs created page Codon list (Created page with "20 Amino acids, their single-letter data-base codes (SLC), and their corresponding DNA codons {| class="wikitable" |+ !Amino Acid !SLC !DNA codons |- |Isoleucine |I |ATT, ATC, ATA |- |Leucine |L |CTT, CTC, CTA, CTG, TTA, TTG |- |Valine |V |GTT, GTC, GTA, GTG |- |Phenylalanine |F |TTT, TTC |- |Methionine |M |ATG |- |Cysteine |C |TGT, TGC |- |Alanine |A |GCT, GCC, GCA, GCG |- |Glycine |G |GGT, GGC, GGA, GGG |- |Proline |P |CCT, CCC, CCA, CCG |- |Threonine |T |ACT, ACC, ACA...")
15:36, 4 August 2025 WikiSysop talk contribs created page File:DNA.jpg
15:36, 4 August 2025 WikiSysop talk contribs uploaded File:DNA.jpg
15:32, 4 August 2025 WikiSysop talk contribs created page Biological knowledge needed in the course (Created page with "__NOTOC__ == Genetic information == The genetic information is stored in the DNA double helix strand, check [https://en.wikipedia.org/wiki/DNA Wikipeida on DNA]. A strand consists of a sequence of the 4 nucleotides (bases); Adenine (A), Thymine (T), Cytosine (C) and Guanine (G). A gene is a sequence of the 4 different nucleotides, where subsequent triplets of nucleotides (a codon) is translated into a sequence of amino acids, which then forms the proteins of our body. A...")
15:31, 4 August 2025 WikiSysop talk contribs created page Good code (Created page with "Good code is both '''Correct''' and have good '''Quality'''. === Correctness === This is simply to which degree does the solution(s) give the right answer when using the data set supplied with the exercise - '''or''' similar natural data sets. "Natural data sets" in this context are data set, that * are NOT specially constructed to catch minor flaws in the programming. * do NOT differ significantly from what has been used in exercises. * are NOT unlikely to occur in...")
15:29, 4 August 2025 WikiSysop talk contribs created page AI guidelines for the course (Created page with "It is strongly preferred that you do '''not''' use AI in the course. The skills you need to acquire are best acquired by your own effort or perhaps in a discussion with a fellow student or TA/teacher. However, a proper responsible use of AI can to some extent replace a discussion with a fellow human. The purpose of AI in the course is to help you learn - not to solve your problems for you - possibly (likely) in a way you do not understand. DTU's honour code is t...")
15:22, 4 August 2025 WikiSysop talk contribs created page Course Survival Guide (Created page with "__NOTOC__ == Introduction == Completing your studies at the Technical University of Denmark will earn you the title “Engineer”. An engineer is assumed to have passed a series of courses covering core engineering competencies, one of which is basic programming. But why should you learn basic programming? Technology development within the biotech- and pharma- industries and research has resulted in a data output far surpassing what standard tools such as Excel is able...")
15:09, 4 August 2025 WikiSysop talk contribs created page How the course is conducted (Created page with "__NOTOC__ Weekly exercises are given every Monday. This constitutes an exercise set. There will be 13 of those. Exercises have to be uploaded to "DTU Learn" latest Sunday in the week after the exercises were given, i.e you have 7 days to complete a set. Peer evaluation of exercises are done in the following week to be handed in Friday. The evaluations are mandatory. At least 11 of 13 evaluations must be handed in - in time - for you to be allowed to take the...")
14:44, 4 August 2025 WikiSysop talk contribs created page Programme (Created page with "'''Collection of files''' used in the exercises and lessons - all gathered here. * 03/09 Lesson 1: Python recap * 10/09 Lesson 2: The path and simple file reading * 17/09 Lesson 3: Pseudo code and comments * 24/09 Lesson 4: String manipulation * 01/10 Lesson 5: Exceptions and bug handling * 08/10 Lesson 6: Stateful parsing, [https://evaluering.dtu.dk/ Midterm evaluation] - part 1 * Fall holidays * 22/10 Lesson 7 Fun...")
13:45, 4 August 2025 WikiSysop talk contribs deleted page Main Page (content was: "MediaWiki has been installed. 22116/22166 Python programming in Life Science Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software. == Getting started == * [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list] * [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ] * [https://lists.wikimedia.org/post...")
13:44, 4 August 2025 WikiSysop talk contribs created page MediaWiki:Mainpage (Created page with "22116/22166_Python_programming_in_Life_Science")
13:42, 4 August 2025 WikiSysop talk contribs created page MediaWiki:Sidebar (Created page with " * navigation ** https://teaching.healthtech.dtu.dk/|Course List ** https://teaching.healthtech.dtu.dk/22116/|22116/22166 ** Programme|Programme * TOOLBOX")
13:40, 4 August 2025 WikiSysop talk contribs created page 22116/22166 Python programming in Life Science (Created page with "Info on 22116")
13:36, 4 August 2025 WikiSysop talk contribs created page MediaWiki:Disclaimers (Created blank page)
13:36, 4 August 2025 WikiSysop talk contribs created page MediaWiki:Aboutsite (Created blank page)
13:32, 4 August 2025 WikiSysop talk contribs created page MediaWiki:Privacy (Created blank page)

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