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26 September 2025
- 13:4313:43, 26 September 2025 diff hist +5,509 N 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..." current
- 13:4113:41, 26 September 2025 diff hist +3,133 N 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..." current
- 13:4013:40, 26 September 2025 diff hist 0 m Resistance to antibiotics →Input and output current
- 13:3913:39, 26 September 2025 diff hist 0 N File:Absent.jpg No edit summary current
- 13:3913:39, 26 September 2025 diff hist 0 N File:Present.jpg No edit summary current
- 13:3113:31, 26 September 2025 diff hist 0 N File:Ngs-coverage-depth.jpg No edit summary current
- 13:2513:25, 26 September 2025 diff hist +7,356 N 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.<br> Given a "database" of bacterial resistance genes as a fasta file and a FASTQ file where a metagenomics sample..."
- 13:2313:23, 26 September 2025 diff hist +6,642 N 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..." current
- 13:2313:23, 26 September 2025 diff hist 0 m Text mining MEDLINE abstracts →Input and output current
- 13:2213:22, 26 September 2025 diff hist 0 m K-means clustering →Details current
- 13:2113:21, 26 September 2025 diff hist +2,965 N 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..." current
- 13:1913:19, 26 September 2025 diff hist +5,175 N 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,..." current
- 13:1713:17, 26 September 2025 diff hist +2,619 N 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..."
- 13:1713:17, 26 September 2025 diff hist +3,309 N 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..."
- 13:1413:14, 26 September 2025 diff hist +597 N 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..." current
- 13:1213:12, 26 September 2025 diff hist +11,482 N 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.<br> Tip: <span style="color:red">If you want your peer to pay specific attention to someth..." current
- 13:1113:11, 26 September 2025 diff hist −3,580 m Aligning expectations →Passing the course
- 13:0513:05, 26 September 2025 diff hist +1 m Aligning expectations →Special expectations
- 13:0413:04, 26 September 2025 diff hist −22 m Aligning expectations →Fulfilling prerequisites
- 13:0313:03, 26 September 2025 diff hist +27,201 N 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.<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..."
- 13:0013:00, 26 September 2025 diff hist +9 m 22118/22168 Advanced Unix & Python for Bioinformaticians →Course details
- 12:5912:59, 26 September 2025 diff hist +5,217 m 22118/22168 Advanced Unix & Python for Bioinformaticians No edit summary
4 August 2025
- 14:1414:14, 4 August 2025 diff hist +130 m 22118/22168 Advanced Unix & Python for Bioinformaticians No edit summary
- 14:1114:11, 4 August 2025 diff hist +22 m 22118/22168 Advanced Unix & Python for Bioinformaticians No edit summary
- 13:5313:53, 4 August 2025 diff hist +56 N MediaWiki:Mainpage Created page with "22118/22168 Advanced Unix & Python for Bioinformaticians" current
- 13:5113:51, 4 August 2025 diff hist +13 N 22118/22168 Advanced Unix & Python for Bioinformaticians Created page with "Info on 22118"
- 13:5113:51, 4 August 2025 diff hist +153 N MediaWiki:Sidebar Created page with "* navigation ** https://teaching.healthtech.dtu.dk/|Course List ** https://teaching.healthtech.dtu.dk/22118/|22118/22168 ** Programme|Programme * TOOLBOX" current
- 13:5013:50, 4 August 2025 diff hist 0 N MediaWiki:Disclaimers Created blank page current
- 13:4913:49, 4 August 2025 diff hist 0 N MediaWiki:Aboutsite Created blank page current
- 13:4913:49, 4 August 2025 diff hist 0 N MediaWiki:Privacy Created blank page current