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21:42, 14 November 2024 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...")
17:13, 1 March 2024 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...")
17:12, 1 March 2024 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...")
17:11, 1 March 2024 WikiSysop talk contribs created page How the course is conducted (Created page with "__NOTOC__ Weekly exercises are given every Tuesday. 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 6 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...")
17:09, 1 March 2024 WikiSysop talk contribs created page Programme 2023 (Created page with "'''Collection of files''' used in the exercises and lessons - all gathered here. * 29/08 Lesson 1: Using Jupyter Notebook * 05/09 Lesson 2: Python Basics * 12/09 Lesson 3: Simple File Reading * 19/09 Lesson 4: Pseudocode and Comments * 26/09 Lesson 5: Python Input-Output * 03/10 Lesson 6: Exceptions and Bug Handling, [https://evaluering.dtu.dk/ Midterm evaluation] - part 1 * 10/10 Lesson 7 Stateful Parsing, [https://evaluering.dtu.dk/ Mid...")
17:08, 1 March 2024 WikiSysop talk contribs created page File:Correlation.png
17:08, 1 March 2024 WikiSysop talk contribs uploaded File:Correlation.png
17:08, 1 March 2024 WikiSysop talk contribs created page File:Alfabeta.png
17:08, 1 March 2024 WikiSysop talk contribs uploaded File:Alfabeta.png
17:07, 1 March 2024 WikiSysop talk contribs created page File:Calc.png
17:07, 1 March 2024 WikiSysop talk contribs uploaded File:Calc.png
17:06, 1 March 2024 WikiSysop talk contribs created page File:StandardDeviation.gif
17:06, 1 March 2024 WikiSysop talk contribs uploaded File:StandardDeviation.gif
17:05, 1 March 2024 WikiSysop talk contribs created page How to Python (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Dictionaries |Next: Programme |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_14-HowTo.ppt How to python] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=af34544c-2273-4b84-9c7f-af27012c8ac4 Common beginner mistakes] == Subjects covered == Various mistakes and bad ideas, not well t...")
17:01, 1 March 2024 WikiSysop talk contribs created page Example code - Dicts (Created page with "__NOTOC__ == Files used in example == [http://teaching.healthtech.dtu.dk/material/36610/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-...")
17:01, 1 March 2024 WikiSysop talk contribs created page Dictionaries (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Sets |Next: How to Python |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_13-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/Viewer.aspx?id=7b897492-bedb-4042-a4fc...")
17:00, 1 March 2024 WikiSysop talk contribs created page Sets (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 == Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=e69a7b62-4f83-4b92-b254-af27012c464e Sets] Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_12-Sets.ppt Sets] == Subjects covered == * Sets, which are unordered data collections with no dupli...")
17:00, 1 March 2024 WikiSysop talk contribs created page Simple Pattern Matching (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: More with Lists |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, strippi...")
17:00, 1 March 2024 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...")
16:59, 1 March 2024 WikiSysop talk contribs created page More with Lists (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Lists/Sequences |Next: Simple Pattern Matching |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_10-MoreLists.ppt More with Lists] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=b253adf9-282f-4885-9ce3-af27012d346e More advanced methods with lists] Video: [https://panopto.dtu.dk/Pano...")
16:58, 1 March 2024 WikiSysop talk contribs created page Lists/Sequences (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Stateful Parsing |Next: More with Lists |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_09-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/Panopto/Pages/...")
16:58, 1 March 2024 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/Sequences |} == 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/P...")
16:54, 1 March 2024 WikiSysop talk contribs created page File:BullsEye.png
16:54, 1 March 2024 WikiSysop talk contribs uploaded File:BullsEye.png
16:54, 1 March 2024 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...")
16:53, 1 March 2024 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: Python Input-Output |Next: Stateful Parsing |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_07-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/Pages/Vi...")
16:52, 1 March 2024 WikiSysop talk contribs created page Example code - Input Output (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...")
16:47, 1 March 2024 WikiSysop talk contribs created page File:DNA.jpg
16:47, 1 March 2024 WikiSysop talk contribs uploaded File:DNA.jpg
16:44, 1 March 2024 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...")
16:44, 1 March 2024 WikiSysop talk contribs created page Python Input-Output (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/22101/22101_06-InputOutput.ppt Input, output, libraries and strings] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=0f769984-a650-444f-bb2c-af27012e79b3 File reading and writing] Video: [...")
16:42, 1 March 2024 WikiSysop talk contribs created page File:Shapes.png
16:42, 1 March 2024 WikiSysop talk contribs uploaded File:Shapes.png
16:33, 1 March 2024 WikiSysop talk contribs created page Pseudocode and Comments (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Simple File Reading |Next: Python Input-Output |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_05-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 comments] Res...")
16:33, 1 March 2024 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...")
16:32, 1 March 2024 WikiSysop talk contribs created page Simple File Reading (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Python Basics |Next: Pseudocode and Comments |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_04-FileReading.ppt Simple File Reading] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=e51d5f37-84e5-46d4-8252-af270129a697 Simple file reading] Video: [https://panopto.dtu.dk/Panopto/Pages...")
16:32, 1 March 2024 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...")
16:31, 1 March 2024 WikiSysop talk contribs created page Python Basics (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Using Jupyter Notebook |Next: Simple File Reading |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_03-Basics.ppt Python Basics] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=2bea1663-7677-442a-8802-af27012a12ab Python basics. Language function. Assignment] Video: [https://panopto.d...")
16:30, 1 March 2024 WikiSysop talk contribs created page Using Jupyter Notebook (Created page with "__NOTOC__ {| width=500 style="float:right; margin-left: 10px; margin-top: -56px;" |Previous: Programme |Next: Python Basics |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_01-InstallingJupyter.ppt Installing Jupyter] - installing Anaconda which has the Notebook Powerpoint: [https://teaching.healthtech.dtu.dk/material/22101/22101_02-Jupyter.ppt Using Jupyter Notebook] PDF: [https://teac...")
16:30, 1 March 2024 WikiSysop talk contribs created page Collection of files (Created page with "__NOTOC__ Last updated: September 2, 2022 == 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 together in one convenient download for you. [https://te...")
16:29, 1 March 2024 WikiSysop talk contribs created page Programme (Created page with "'''Collection of files''' used in the exercises and lessons - all gathered here. * 29/08 Lesson 1: Using Jupyter Notebook * 05/09 Lesson 2: Python Basics * 12/09 Lesson 3: Simple File Reading * 19/09 Lesson 4: Pseudocode and Comments * 26/09 Lesson 5: Python Input-Output * 03/10 Lesson 6: Exceptions and Bug Handling, [https://evaluering.dtu.dk/ Midterm evaluation] - part 1 * 10/10 Lesson 7 Stateful Parsing, [https://evaluering.dtu.dk/ Mid...")
16:28, 1 March 2024 WikiSysop talk contribs created page Install Jupyter Notebook (Created page with "__NOTOC__ You can install Jupyter Notebook in a number of ways, but the absolute simplest is to install Anaconda, which will give you the Notebook, Python and a number of scientific libraries. There are many resources on the net about how to use Jupyter Notebook, Python and Anaconda itself. The difference between installing Anaconda on Mac and Windows is insignificant, so Mac users can easily figure out how by reading the powerpoint or watching the videos. Link: [h...")
16:23, 1 March 2024 WikiSysop talk contribs created page MediaWiki:Sidebar (Created page with " * navigation ** https://teaching.healthtech.dtu.dk/|Course List ** https://teaching.healthtech.dtu.dk/22101/|22101/22161 ** Programme|Programme * TOOLBOX")
16:20, 1 March 2024 WikiSysop talk contribs created page 22101/22161 - Introduction to programming in Life Science using Python (Created page with "__NOTOC__ '''Teacher:''' [https://www.inside.dtu.dk/da/dtuinside/generelt/telefonbog/person?id=816&cpid=214027&tab=2&qt=dtupublicationquery Peter Wad Sackett], pwsa@dtu.dk  '''Language:''' The course is taught in English. '''Tools:''' The course is using Jupyter Notebook. Install Jupyter Notebook before you meet in class. '...")
16:19, 1 March 2024 WikiSysop talk contribs created page MediaWiki:Mainpage (Created page with "22101/22161 - Introduction to programming in Life Science using Python")
16:18, 1 March 2024 WikiSysop talk contribs created page MediaWiki:Disclaimers (Created blank page)
16:17, 1 March 2024 WikiSysop talk contribs created page MediaWiki:Aboutsite (Created blank page)
16:17, 1 March 2024 WikiSysop talk contribs created page MediaWiki:Privacy (Created blank page)
16:13, 1 March 2024 MediaWiki default talk contribs created page Main Page

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