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6 March 2024
- 15:3515:35, 6 March 2024 diff hist +2,873 N Collection of files Created page with "__NOTOC__ Last updated: February 2, 2023 == 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.<br> You can play around with these files as much as you like. If you change or destroy them, just download them again.<br> Put the files in your course folder on your computer.<br> <!-- The files have been zipped together in one convenient download for you.<br> [https:..." current
- 15:3415:34, 6 March 2024 diff hist +662 N Mini projects Created page with "This is a list of small projects. Making the code for each project should be possible within a day or two (full time). No solutions exists for these projects, nor will they be made. * Project 1: Score sequence data with a PSSM * Project 2: Human genes with activities in more than one region of the cell * Project 3: Heuristic methods for fair sharing * Project 4: Find the mature part of human genes with a signal peptide * Project 5: Find short virus gen..." current
- 15:3315:33, 6 March 2024 diff hist +1,654 N Programme - Spring 2023 Created page with "'''Collection of files''' used in the exercises and lessons - all gathered here. * M 30/01 Lesson 1: Unix * T 02/02 More lecture on Unix * M 06/02 Lesson 2: Python Recap and Objects * T 09/02 ''Random numbers'' * M 13/02 Lesson 3: Regular Expressions * T 16/02 Continuing lesson * M 20/02 Lesson 4: Making Functions * T 23/02 Continuing lesson * M 27/02 Lesson 5: Advanced Data Structures and New Data Types * T 02/03 [https://evaluering.dtu.dk/..." current
- 15:3115:31, 6 March 2024 diff hist +1,485 N 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..." current
- 15:3015:30, 6 March 2024 diff hist 0 N File:DNA.jpg No edit summary current
- 15:3015:30, 6 March 2024 diff hist +4,874 N 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..." current
- 15:2415:24, 6 March 2024 diff hist 0 Runtime evaluation of algorithms No edit summary current
- 15:2315:23, 6 March 2024 diff hist +6,875 N Runtime evaluation of algorithms Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Scientific Libraries, Pandas, Numpy |Next: Scientific Libraries, Statistics |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/36610/Python10-Runtime.pptx Runtime evaluation of algorithms]<br> Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=41edc89b-61a5-475d-84d0-af2701271b5d Runtime Ana..."
- 15:2215:22, 6 March 2024 diff hist +2,320 N Good code Created page with "Evaluating code can be done from a number of criteria. In the course we are using two: Correctness and Quality, each have a number of sub criteria. Any evaluation done by teachers will follow this, and when you evaluate your own or your peers code you should use this. === 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.<br> "Natural data sets..." current
- 15:2015:20, 6 March 2024 diff hist +1,832 N Programme Created page with "'''Collection of files''' used in the exercises and lessons - all gathered here. * M 29/01 Lesson 1: Unix * T 01/02 More lecture on Unix * M 05/02 Lesson 2: Python Recap and Objects * T 08/02 Official talk about Random numbers * M 12/02 Lesson 3: Regular Expressions * T 15/02 Continuing lesson * M 19/02 Lesson 4: Making Functions * T 22/02 Unofficial talk about Garbage Collection in Python * M 26/02 Lesson 5: Advanced Data Structures and New Da..."
- 15:1915:19, 6 March 2024 diff hist +681 N Project list Created page with "The list is arranged approximately from lowest to highest difficulty. # Text mining MEDLINE abstracts # K-means clustering # Data mining in NCBI databases # Searching for motifs in sequences # Data analysis # Resistance to antibiotics # k-nearest neighbor (k-NN) continuous variable estimation # Read trimmer for Next-Generation-Sequencing data # QT clustering # Pairwise alignment # Artificial Neural Network <!-- removed projects..."
- 15:1815:18, 6 March 2024 diff hist +8,453 N Basic Programming Skills for Everyone Created page with "You are expected to possess various trivial programming skills and use them for all your hand-ins. You find a list here. == Comments == Comments in code have no influence on the actual running of the program. It can make the understanding of the code easier (or harder) in several ways, both for the author of the program, but also for a causal reader, who must understand/maintain the code. Comments must not be underestimated in their importance for making the code easier..." current
- 15:1715:17, 6 March 2024 diff hist +27,062 N Aligning expectations Created page with "== What is expected from you == === Fulfilling prerequisites === A course like [https://kurser.dtu.dk/course/22101 22101/22161 Introduction to programming in Life Science using Python] should enable you for this course.<br> Generally speaking, you must know simple Python well, which means you know the basic syntactical structure of Python (assignment, expressions, if, for while, some functions/methods), some data types (integer, float, string, lists, sets, dicts), and tr..."
- 15:1515:15, 6 March 2024 diff hist +9,865 N Course preparation Created page with "Before you meet up on the first day of the course, you will '''have''' to be able to start a terminal in a '''unix''' environment, and to '''edit''' files in the same environment with a text editor. Here is how and what you should do on various Operation Systems (OS). Anything mentioned here is free software. == General remarks about programming environments, IDE's == Some people have discovered tools like Spyder, Jupyter or PyCharm, which creates an environment for mak..."
- 15:1415:14, 6 March 2024 diff hist +5,303 N 22113/22163 - Unix & Python Programming for Bioinformaticians Created page with "__NOTOC__ == Prepare for the course == You must read and follow the Course preparation before the you show up on the first day of the course.<br> You are '''required''' to read at least the first part of Aligning expectations when the course starts and whenever you have a question related to the conduction of the course.<br> Resources can be good to check out during the course, or when you need something more. '''Teacher:''' [https://www.inside.dtu.dk/da/dtuinsi..."
- 15:1315:13, 6 March 2024 diff hist +154 N MediaWiki:Sidebar Created page with " * navigation ** https://teaching.healthtech.dtu.dk/|Course List ** https://teaching.healthtech.dtu.dk/22113/|22113/22163 ** Programme|Programme * TOOLBOX" current
- 15:1215:12, 6 March 2024 diff hist +61 N MediaWiki:Mainpage Created page with "22113/22163 - Unix & Python Programming for Bioinformaticians" current
- 15:1015:10, 6 March 2024 diff hist 0 N MediaWiki:Disclaimers Created blank page current
- 15:1015:10, 6 March 2024 diff hist 0 N MediaWiki:Aboutsite Created blank page current
- 15:1015:10, 6 March 2024 diff hist 0 N MediaWiki:Privacy Created blank page current
