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16:21, 11 February 2026 WikiSysop talk contribs created page Solo git (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Intermediate unix |Next: Collaborative git |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_03-Git.ppt Git]  == Subjects covered == * GitHub - short * Git - concepts == Exercises to be handed in == '''In exercises 2-9 the job i...")
09:54, 27 January 2026 WikiSysop talk contribs created page Last words (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Changing existing code base |Next: Programme |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_13-LastWords.ppt Last words]  == Subjects covered == Course summery Standard libraries Third party libraries Optimization<...")
09:50, 27 January 2026 WikiSysop talk contribs created page Runtime evaluation (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Intermediate unit test |Next: Changing existing code base |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/Python10-Runtime.pptx Runtime evaluation of algorithms] Old ppt, not so important Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=41edc89b-61a5-475d-84d0-af2701271b5d Run...")
09:41, 27 January 2026 WikiSysop talk contribs created page Example code - Unit test (Created page with "I decided to make some unit tests for my prime number generator, I used as an example last week, see Example code - Classes I make two files - one file containing the class ''PrimeGenerator.py'' and one file containing the tests, ''test_PrimeGenerator.py''. The files are supposed to be in the same folder. I will not show the code from last week in ''PrimeGenerator.py'', if you want to see the code, click the above link. This is my unit test file. I want to test...")
09:36, 27 January 2026 WikiSysop talk contribs created page Beginning unit test (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Intermediate classes |Next: Intermediate unit test |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_09-Testing.ppt Testing] Online: [https://docs.pytest.org/ pytest documentation] Resource: Example code - Unit test Resource: Unit test - start of reverse polish notation...")
09:32, 27 January 2026 WikiSysop talk contribs created page Example code - Classes (Created page with "You know how I often use primes in my examples, so I decided to make a prime number generator class as an example. It is able to generate a range of primes, somewhat similar to the way '''range()''' works. Wanting to be smart, I decided to store the primes I have already computed in a class variable, so I do not have to compute them again at least while the program runs. I am doing a running incremental calculation of primes, storing them as I find them, and...")
09:32, 27 January 2026 WikiSysop talk contribs created page Beginning classes (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Comprehension, generators, iteration |Next: Intermediate classes |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_07-Classes.ppt Classes] Resource: Example code - Classes == Subjects covered == Classes Object Oriented Programming == Exercises to be handed in == The exe...")
09:29, 27 January 2026 WikiSysop talk contribs created page Example code - Misc (Created page with "__NOTOC__ == Files used in example == Our favorite data file: ''ex1.dat'' == Closest to zero == There are a lot of numbers in this file. Which number is the closest to zero and where is it (row/column) ? This is more complicated because there are both positive and negative numbers in the file. In order to demonstrate some of the new functions/methods, I pull the entire file into memory. This problem could be solved by reading line-by-line and not keeping all the...")
09:27, 27 January 2026 WikiSysop talk contribs created page Example code - Comprehension (Created page with "__NOTOC__ == Files used in example == [http://teaching.healthtech.dtu.dk/material/22118/TA_list.txt TA_list.txt] [http://teaching.healthtech.dtu.dk/material/22118/student_list.txt student_list.txt] == Assigning students to TA's, Take 2 == After having used the original program a few times, see [https://teaching.healthtech.dtu.dk/22116/index.php/Example_code_-_Complex_data here], I got dissatisfied with it - the randomness did not ensure even distribution of stud...")
09:21, 27 January 2026 WikiSysop talk contribs created page Comprehension, generators, iteration (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Functions, namespace, memory management |Next: Beginning classes |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_06-Comprehension.ppt Comprehension, generators & iteration] Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_06-Random.ppt Randomness] Video: [ht...")
09:12, 27 January 2026 WikiSysop talk contribs created page Example code - Functions (Created page with "__NOTOC__ == File used in example == [http://teaching.healthtech.dtu.dk/material/22118/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...")
09:11, 27 January 2026 WikiSysop talk contribs created page Functions, namespace, memory management (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: More git |Next: Comprehension, iteration, generators |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_05-Functions.ppt Functions] - this will be short as it is a reminder. Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_05-Namespace.ppt Namespace]. Powerpoin...")
09:04, 27 January 2026 WikiSysop talk contribs created page 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. 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:...")
14:21, 7 November 2025 WikiSysop talk contribs created page Intermediate Unix (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: None |Next: Python Recap and Objects |} You did do the Course preparation, right!! Otherwise all of this matters not. == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] == Subjects covered == * New Unix commands * Scripting in bash == Exercises to be...")
12:05, 6 November 2025 WikiSysop talk contribs created page Beginning Unix (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Programme |Next: Intermediate Unix |} You did do the Course preparation, right!! Otherwise all of this matters not. == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] The videos are not entirely in sync with the powerpoint, as it has been updated.<...")
14:37, 17 October 2025 WikiSysop talk contribs created page 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, VScode or PyCharm, which creates an environment...")
12:05, 17 October 2025 WikiSysop talk contribs created page Programme (Created page with "'''Collection of files''' used in the exercises and lessons - all gathered here. * 01/09 Lesson 1: Beginning Unix * 08/09 Lesson 2: intermediate Unix * 15/09 Lesson 3: Git on command line * 22/09 Lesson 4: More Git * 29/09 Lesson 5: Functions, scope, garbage collection * 06/10 Lesson 6: Comprehension, iteration, generators, [https://evaluering.dtu.dk/ Midterm evaluation] - part 1 * Fall holidays * 20/10 Lesson 7 Beg...")
13:34, 26 September 2025 WikiSysop talk contribs created page File:DNA.jpg
13:34, 26 September 2025 WikiSysop talk contribs uploaded File:DNA.jpg
13:33, 26 September 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...")
13:32, 26 September 2025 WikiSysop talk contribs created page Shortest path in graph (Created page with "__NOTOC__ === Description === The program is given as input a file containing connected nodes in a graph and a weight assigned to the edge between the nodes. The program shall answer the questions: Is there a path between two given nodes in the graph? If so, what is the shortest path ? This is useful in a number of situations: Protein interaction, which proteins interact together, thereby discovering f.ex. new pathways. Social networks, who knows who, proving the "si...")
13:31, 26 September 2025 WikiSysop talk contribs created page Positive proteins (Created page with "__NOTOC__ === Description === Find the top 1000 most positively charged protein sequences in uniprot and put them in a fasta file. Repeat the search but this time find the most positively charged protein sequences per molecular weight of the sequence and put that into another fasta file. Among the 20 common amino acids, five have a side chain which can be charged. At pH=7, two are negative charged: aspartic acid (D) and glutamic acid (E) (acidic side chains), and three a...")
13:30, 26 September 2025 WikiSysop talk contribs created page Spider toxins (Created page with "__NOTOC__ === Description === Find all spider toxins in uniprot and output them in a fasta file. Who knows when it will be useful to produce venom? === Input/output === Download the entire [https://teaching.healthtech.dtu.dk/material/22118/uniprot_sprot.dat.gz swissprot database]. This will be your input file to your program. Unpack it yourself with gunzip uniprot_sprot.dat.gz or whatever method you prefer. Careful, it will take up 3 GB. Notice there are many s...")
13:29, 26 September 2025 WikiSysop talk contribs created page Fun with biology - find english words (Created page with "__NOTOC__ === Description === Parse the entire uniprot database and extract the ID and the sequences. Find English words that are hidden (actually occur randomly) in the sequences. The words must be between 3 and 10 letters long, both inclusive. Display or save in a file the ID together with the words found in the sequence, but only if the total number of letters is 5 or more for that entry. === Input/output === Download the entire [https://teaching.healthtech.dtu.dk/ma...")
13:28, 26 September 2025 WikiSysop talk contribs created page Find short virus genes with disulfid bridges (Created page with "__NOTOC__ === Description === Find all short (150 or less aa) virus genes in uniprot, that contain intrachain disulfid bridges. Interchain disulfide bonds can produce stable, covalently linked protein dimers, multimers or complexes, whereas intrachain disulfide bonds can contribute to protein folding and stability. === Input/output === Download the entire [https://teaching.healthtech.dtu.dk/material/22118/uniprot_sprot.dat.gz swissprot database]. This will be your input...")
13:27, 26 September 2025 WikiSysop talk contribs created page Find the mature part of human genes with a signal peptide (Created page with "__NOTOC__ === Description === Find all human genes in uniprot with a signal peptide. Extract the entire sequence and create a fasta file with only the mature proteins. === Input/output === Download the entire [https://teaching.healthtech.dtu.dk/material/22118/uniprot_sprot.dat.gz swissprot database]. This will be your input file to your program. Unpack it yourself with gunzip uniprot_sprot.dat.gz or whatever method you prefer. Careful, it will take up 3 GB. Not...")
13:26, 26 September 2025 WikiSysop talk contribs created page Heuristic methods for fair sharing (Created page with "__NOTOC__ === Description === Distributing jobs/items to a number of consumers in a fair way has a number of applications. In this project you must implement 5 methods mentioned in the [https://teaching.healthtech.dtu.dk/material/22112/HPCLife-LoadBalancing.ppt powerpoint]: Random Assignment, Round Robin, Max-Min Round Robin, Reverse Round Robin and Least Load. === Input/output === As can be seen from the powerpoint, there is some randomness in the input, i.e. the numb...")
13:25, 26 September 2025 WikiSysop talk contribs created page Human genes with activities in more than one region of the cell (Created page with "__NOTOC__ === Description === Find human genes which are targeted to more than one region in the cell. Save the genes in fasta format. === Input/output === Download the entire [https://teaching.healthtech.dtu.dk/material/22118/uniprot_sprot.dat.gz swissprot database]. This will be your input file to your program. Unpack it yourself with gunzip uniprot_sprot.dat.gz or whatever method you prefer. Careful, it will take up 3 GB. Notice there are many swissprot entr...")
13:24, 26 September 2025 WikiSysop talk contribs created page Score sequence data with a PSSM (Created page with "__NOTOC__ === Description === Position specific scoring matrices (PSSM) are statistically motivated sequence motif models that provide higher sensitivity and specificity than regular expressions. The project consists of reading a TRANSFAC matrix table, converting it to a log-likelihood matrix, which is used to find matching motifs in a DNA fasta file. Learn more about PSSM: https://en.wikipedia.org/wiki/Position_weight_matrix === Input and output === The program is giv...")
13:22, 26 September 2025 WikiSysop talk contribs created page 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...")
12:48, 26 September 2025 WikiSysop talk contribs created page Artificial Neural Network (Created page with "__NOTOC__ ===Description=== Implement a simple artificial neural network algorithm with backpropagation in Python. ANNs are of great interest in bioinformatics. The institute has created many online prediction servers, which utilises ANNs. The data is a part of a project at DTU HealthTech, which is about prediction of whether certain variations of a SNP will lead to a disease or not. A lot of work has already gone into preparing a data set for network training. The r...")
12:47, 26 September 2025 WikiSysop talk contribs created page Pairwise alignment (Created page with "__NOTOC__ ===Description=== Aligning sequences is of great importance in bioinformatics. Many discoveries are based on finding sequences that align to each other. Evolution theory and phylogeny are based on sequence alignments. This project is about implementing a well-known algorithm for aligning two sequences, i.e. finding where they match in an optimal fashion. You must choose to implement either: # Smith-Waterman alignment where the goal is to find the best local al...")
12:45, 26 September 2025 WikiSysop talk contribs created page QT clustering (Created page with "__NOTOC__ ===Description=== The program reads a number of data points (multi-dimensional vectors) from a file and partitions those into clusters. Clustering is important in discovering patterns or modes in multi-dimensional data sets. It is also a method of organizing data examples into similar groups (clusters). In this particular case, QT clustering partitions the data set such that each example (data point) is assigned to exactly one cluster. QT clustering is superior...")
12:43, 26 September 2025 WikiSysop talk contribs created page Read trimmer for Next-Generation-Sequencing data (Created page with "__NOTOC__ ===Description=== The advent of Next Generation Sequencing (NGS) technologies have transformed how biological research is being performed and today almost all biological fields use the technology for cutting edge discoveries. Today, a human genome can be sequenced in very short time for approximately $1000 giving unprecedented possibilities for investigating human traits, evolution and diseases. Similarly whole bacterial communities and their interplay with the...")
12:41, 26 September 2025 WikiSysop talk contribs created page K-nearest neighbor (k-NN) continuous variable estimation (Created page with "__NOTOC__ ===Description=== This scripts read a matrix-styled data file, containing missing values, and infers these values by finding the k-nearest neighbors. An application of this can be seen in Microarray experiments, in which the observed signal is not always significantly different from the background signal. Imputing these values are a cheaper solution rather than redoing the whole experiment. This method has been shown to perform better than e.g. rowmeans, and fa...")
12:39, 26 September 2025 WikiSysop talk contribs created page File:Absent.jpg
12:39, 26 September 2025 WikiSysop talk contribs uploaded File:Absent.jpg
12:39, 26 September 2025 WikiSysop talk contribs created page File:Present.jpg
12:39, 26 September 2025 WikiSysop talk contribs uploaded File:Present.jpg
12:31, 26 September 2025 WikiSysop talk contribs created page File:Ngs-coverage-depth.jpg
12:31, 26 September 2025 WikiSysop talk contribs uploaded File:Ngs-coverage-depth.jpg
12:25, 26 September 2025 WikiSysop talk contribs created page Resistance to antibiotics (Created page with "__NOTOC__ ===Description=== Bacterial resistance to antibiotics is a growing problem, and there is many real life scenarios where it is important to understand what type antibiotics will be effective on a patient or what kind of resistance can be expected in certain bacterial populations - or even what kind of antibiotics has the farmer been feeding his pigs. Given a "database" of bacterial resistance genes as a fasta file and a FASTQ file where a metagenomics sample...")
12:23, 26 September 2025 WikiSysop talk contribs created page Data analysis (Created page with "__NOTOC__ ===Description=== This project is about analyzing specific data and answer various questions about it. The data file is a flat file database constructed in year 2000 with various information about people, and can be seen here as [https://teaching.healthtech.dtu.dk/material/22118/people.db people.db]. The program must read this file ONCE - line by line - not storing the actual lines for future reference, but entering the data in an appropriate data structure of...")
12:21, 26 September 2025 WikiSysop talk contribs created page Searching for motifs in sequences (Created page with "__NOTOC__ ===Description=== A sequence motif is typically a short sequence pattern of DNA or amino acid sequence that is conserved across various gene families or organisms. Sequence motifs are recognizable and could be a promoter, a binding site or a domain that folds into a specific structure. The mechanism for finding motifs is often Hidden Markov Models or Neural Networks, which both require a lot of examples of the motif to work, but here you will explore a differen...")
12:19, 26 September 2025 WikiSysop talk contribs created page Data mining in NCBI databases (Created page with "__NOTOC__ ===Description=== Mine NCBI databases for networks of genes which are connected by the fact that they have been mentioned in the same PubMed article. This project is a good example of how research can be done in Real Life and contains a high degree of freedom in how you want to proceed. Part of the problem is to understand and subsequently parse the NCBI databases, which are flat files. The information found could be used for pathway analysis and construction,...")
12:17, 26 September 2025 WikiSysop talk contribs created page K-means clustering (Created page with "__NOTOC__ ===Description=== The program reads a number of data points (multi-dimensional vectors) from a file and partitions those into K clusters. Clustering is important in discovering patterns or modes in multi-dimensional data sets. It is also a method of organizing data examples into similar groups (clusters). In this particular case, K-means partitions the data set such that each example (data point) is assigned to exactly one cluster - the one with the closest cen...")
12:17, 26 September 2025 WikiSysop talk contribs created page Text mining MEDLINE abstracts (Created page with "__NOTOC__ === Description === The purpose is to mine MEDLINE abstracts for words which are associated with each other. This is done by finding ''informative'' words that co-occur with each other, i.e. the words would be in the same abstract. The process consists of a number of steps, where the first step is to find the non-informative words in the abstracts. Second step will be parsing the abstracts again disregarding the non-informative words, and create some occurrence...")
12:14, 26 September 2025 WikiSysop talk contribs created page Project list (Created page with "Remember to [https://teaching.healthtech.dtu.dk/22118/index.php/Aligning_expectations#Projects,_general_information read about projects here]. 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...")
12:12, 26 September 2025 WikiSysop talk contribs created page Code construction (Created page with "Learning how to construct good code is a main goal of the course. An important tool to facilitate this is peer evaluation. It is beneficial for you both to evaluate others, seeing other ways of solving the same problem - and to get feedback from other people on your own work. When evaluating you should check the teachers solutions to have some kind of reference apart from your own. Tip: If you want your peer to pay specific attention to someth...")
12:03, 26 September 2025 WikiSysop talk contribs created page Aligning expectations (Created page with "== What is expected from you == === Fulfilling prerequisites === A course like [https://kurser.dtu.dk/course/22116 22116/22166 Introduction to programming in Life Science using Python] should enable you for this course. 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...")

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