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15:02, 13 March 2024 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...")
17:00, 6 March 2024 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...")
16:24, 6 March 2024 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...")
16:23, 6 March 2024 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/22113/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...")
16:22, 6 March 2024 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...")
16:21, 6 March 2024 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/22113/uniprot_sprot.dat.gz swissprot database]. This will be your input...")
16:19, 6 March 2024 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/22113/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...")
16:18, 6 March 2024 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...")
16:13, 6 March 2024 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/36610/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...")
16:10, 6 March 2024 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...")
16:09, 6 March 2024 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...")
16:09, 6 March 2024 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...")
16:08, 6 March 2024 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...")
16:07, 6 March 2024 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...")
16:07, 6 March 2024 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...")
16:05, 6 March 2024 WikiSysop talk contribs created page File:Absent.jpg
16:05, 6 March 2024 WikiSysop talk contribs uploaded File:Absent.jpg
16:04, 6 March 2024 WikiSysop talk contribs created page File:Present.jpg
16:04, 6 March 2024 WikiSysop talk contribs uploaded File:Present.jpg
16:03, 6 March 2024 WikiSysop talk contribs created page File:Ngs-coverage-depth.jpg
16:03, 6 March 2024 WikiSysop talk contribs uploaded File:Ngs-coverage-depth.jpg
15:17, 6 March 2024 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...")
15:16, 6 March 2024 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/22113/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...")
15:16, 6 March 2024 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...")
15:15, 6 March 2024 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,...")
15:15, 6 March 2024 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...")
15:14, 6 March 2024 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...")
15:11, 6 March 2024 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: Scientific Libraries, Plotting |Next: Programme |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_13-LastWords.ppt Last words]  == Subjects covered == Course summery Biopython Optimization Further courses == Exercise...")
15:11, 6 March 2024 WikiSysop talk contribs created page File:Normaldistributionplot.png
15:11, 6 March 2024 WikiSysop talk contribs uploaded File:Normaldistributionplot.png
15:10, 6 March 2024 WikiSysop talk contribs created page File:Picture4.png
15:10, 6 March 2024 WikiSysop talk contribs uploaded File:Picture4.png
15:10, 6 March 2024 WikiSysop talk contribs created page File:Picture3.png
15:10, 6 March 2024 WikiSysop talk contribs uploaded File:Picture3.png
15:10, 6 March 2024 WikiSysop talk contribs created page File:Picture2.png
15:10, 6 March 2024 WikiSysop talk contribs uploaded File:Picture2.png
15:09, 6 March 2024 WikiSysop talk contribs created page File:Picture1.png
15:09, 6 March 2024 WikiSysop talk contribs uploaded File:Picture1.png
15:08, 6 March 2024 WikiSysop talk contribs created page Scientific Libraries, Plotting (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Scientific Libraries, Statistics |Next: Last words |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_12-Plotting.pptx Plotting]  == Subjects covered == matplotlib seaborn == Exercises to be handed in == # Generate a large nu...")
15:08, 6 March 2024 WikiSysop talk contribs created page Scientific Libraries, Statistics (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Runtime evaluation of algorithms |Next: Scientific Libraries, Plotting |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_11-Statistics_SciPy.ppt Statistics, SciPy]  == Subjects covered == Simple statistics with standard python<br...")
15:07, 6 March 2024 WikiSysop talk contribs created page Scientific Libraries, Pandas, Numpy (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Unit test |Next: Runtime evaluation of algorithms |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_09-NumpyPandas.ppt Scientific libraries, Pandas & NumPy] Online: [https://pandas.pydata.org/docs/user_guide/index.html https://pandas.pydata.org/]Pandas documantation Online: [http...")
15:05, 6 March 2024 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. I make two files - one file containing the class and one file containing the tests. The files are supposed to be in the same folder. Notice I changed the name of the class a bit. '''File:''' primegenerator.py <pre> # Prime number generator class primegenerator: # Class varible, known primes in consecutive order, can be extended, but must contain these knownprimes...")
15:04, 6 March 2024 WikiSysop talk contribs created page Unit test (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Classes |Next: Scientific Libraries, Pandas, Numpy |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_08-Testing.ppt Testing] Online: [https://docs.pytest.org/ pytest documentation] Resource: Example code - Unit test Blog: [https://www.joelonsoftware.com/2000/04/30/top-fiv...")
15:02, 6 March 2024 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...")
15:01, 6 March 2024 WikiSysop talk contribs created page Classes (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Comprehension, Generators, Functions and Methods |Next: Unit test |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_07-Classes.ppt Classes] Resource: Example code - Classes == Subjects covered == Classes Object Oriented Programming == Exercises to be handed in == The ex...")
15:00, 6 March 2024 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...")
14:59, 6 March 2024 WikiSysop talk contribs created page Example code - Comprehension (Created page with "__NOTOC__ == Files used in example == [http://teaching.healthtech.dtu.dk/material/22113/TA_list.txt TA_list.txt] [http://teaching.healthtech.dtu.dk/material/22113/student_list.txt student_list.txt] == Assigning students to TA's, Take 2 == After having used the original program a few times, see Example code - Data structures, I got dissatisfied with it - the randomness did not ensure even distribution of students to the various TA's. The TA's got the right nu...")
14:59, 6 March 2024 WikiSysop talk contribs created page Comprehension, Generators, Functions and Methods (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Advanced Data Structures and New Data Types |Next: Classes |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_06-Comprehension.ppt Comprehension, Generators, Functions and Methods] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=ef476c74-cc82-4478-afd2-af270128c92f Compreh...")
14:58, 6 March 2024 WikiSysop talk contribs created page Example code - Data structures (Created page with "== Files used in example == [http://teaching.healthtech.dtu.dk/material/22113/TA_list.txt TA_list.txt] [http://teaching.healthtech.dtu.dk/material/22113/student_list.txt student_list.txt] == Assigning students to TA's, Take 1 == This is a python3 program written by a TA. It was done in a hurry, without much regard to the teaching principles. The purpose of the program is to read a list of students and a list of TA's and randomly assign students to TA's for gradi...")
14:57, 6 March 2024 WikiSysop talk contribs created page Advanced Data Structures and New Data Types (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Making Functions |Next: Comprehension, Generators, Functions and Methods |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_05-DataStructuresTypes.ppt Advanced Data Structures and New Data Types] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=d2ebb169-453f-4370-93b9-af270...")

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