User contributions for WikiSysop

16:0316:03, 6 March 2024 diff hist 0‎ N File:Ngs-coverage-depth.jpg ‎No edit summary current
15:1715:17, 6 March 2024 diff hist +7,287‎ 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. Given a "database" of bacterial resistance genes as a fasta file and a FASTQ file where a metagenomics sample..."
15:1615:16, 6 March 2024 diff hist +5,566‎ 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/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..."
15:1615:16, 6 March 2024 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
15:1515:15, 6 March 2024 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
15:1515:15, 6 March 2024 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..." current
15:1415:14, 6 March 2024 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..." current
15:1115:11, 6 March 2024 diff hist +599‎ N 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..." current
15:1115:11, 6 March 2024 diff hist 0‎ N File:Normaldistributionplot.png ‎No edit summary current
15:1015:10, 6 March 2024 diff hist 0‎ N File:Picture4.png ‎No edit summary current
15:1015:10, 6 March 2024 diff hist 0‎ N File:Picture3.png ‎No edit summary current
15:1015:10, 6 March 2024 diff hist 0‎ N File:Picture2.png ‎No edit summary current
15:0915:09, 6 March 2024 diff hist 0‎ N File:Picture1.png ‎No edit summary current
15:0815:08, 6 March 2024 diff hist +2,700‎ N 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..." current
15:0815:08, 6 March 2024 diff hist +3,632‎ N 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..."
15:0715:07, 6 March 2024 diff hist +4,956‎ N 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..."
15:0515:05, 6 March 2024 diff hist +2,789‎ N 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..."
15:0415:04, 6 March 2024 diff hist +3,087‎ N 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..." current
15:0215:02, 6 March 2024 diff hist +3,793‎ N 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..."
15:0115:01, 6 March 2024 diff hist +5,203‎ N 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..." current
15:0015:00, 6 March 2024 diff hist +1,466‎ N 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..." current
14:5914:59, 6 March 2024 diff hist +12,208‎ N 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..." current
14:5914:59, 6 March 2024 diff hist +6,004‎ N 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..." current
14:5814:58, 6 March 2024 diff hist +4,107‎ N 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..." current
14:5714:57, 6 March 2024 diff hist +5,224‎ N 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..." current
14:4014:40, 6 March 2024 diff hist +3,538‎ N Example code - Functions ‎ Created page with "__NOTOC__ == File used in example == [http://teaching.healthtech.dtu.dk/material/22113/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..." current
14:3914:39, 6 March 2024 diff hist 0‎ N File:StandardDeviation.gif ‎No edit summary current
14:3914:39, 6 March 2024 diff hist +4,178‎ N Making Functions ‎ Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Regular Expressions |Next: Advanced Data Structures and New Data Types |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_04-Functions.ppt Making functions] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=f509116f-48e5-445b-bf6e-af27012ba23f Functions in Python] Monday ..." current
14:3814:38, 6 March 2024 diff hist +4,097‎ N Example code - Regex ‎ Created page with "__NOTOC__ == Files used in example == [http://teaching.healthtech.dtu.dk/material/22113/people.db Database (text file) of people] == Average height of certain people == In the file there are entries like <pre> CPR: 230226-9781 First name: Anton Last name: Gade Height: 201 Weight: 65 Eye color: Black Blood type: A+ Children: 081154-2786 120853-1151 050354-4664 </pre> The problem we want to solve is to find the average height of the people in the file with a user given fi..." current
14:3714:37, 6 March 2024 diff hist +4,543‎ N Regular Expressions ‎ Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Python Recap and Objects |Next: Making Functions |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_03-Regex.ppt Regular expressions in Python] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=04cb2b80-d941-42a5-a632-af27012cd0d7 Regular Expressions] Monday Video: [http..." current
14:3714:37, 6 March 2024 diff hist +4,352‎ N Python Recap and Objects ‎ Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Unix |Next: Regular Expressions |} == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_02-RecapObjects.ppt Python Recap and Objects] Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_02-Random.ppt Random numbers] <!-- Resource: Example code - File Reading --..." current
14:3614:36, 6 March 2024 diff hist +6,454‎ N 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] The videos are not entirely in sync with the powerpoint, as it has been updated.<br..." current
14:3514:35, 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. 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:..." current
14:3414:34, 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
14:3314:33, 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
14:3114:31, 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
14:3014:30, 6 March 2024 diff hist 0‎ N File:DNA.jpg ‎No edit summary current
14:3014:30, 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
14:2414:24, 6 March 2024 diff hist 0‎ Runtime evaluation of algorithms ‎No edit summary current
14:2314:23, 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] Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=41edc89b-61a5-475d-84d0-af2701271b5d Runtime Ana..."
14:2214:22, 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. "Natural data sets..." current
14:2014:20, 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..."
14:1914:19, 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..."
14:1814:18, 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
14:1714:17, 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. 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..."
14:1514:15, 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..."
14:1414:14, 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. 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. Resources can be good to check out during the course, or when you need something more. '''Teacher:''' [https://www.inside.dtu.dk/da/dtuinsi..."
14:1314:13, 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
14:1214:12, 6 March 2024 diff hist +61‎ N MediaWiki:Mainpage ‎ Created page with "22113/22163 - Unix & Python Programming for Bioinformaticians" current
14:1014:10, 6 March 2024 diff hist 0‎ N MediaWiki:Disclaimers ‎ Created blank page current

User contributions for WikiSysop

6 March 2024

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