![rebelScience](/img/default-banner.jpg)
- Видео 34
- Просмотров 449 187
rebelScience
Великобритания
Добавлен 29 фев 2008
Welcome to my channel, dedicated to all things Programming, Bioinformatics, Machine Learning and Open-Source Software. Programming and Bioinformatics are my true passions. I am researching longevity (life extension), cell signaling for tissue and organ regeneration, DNA damage repair.
In my work I only use 100% Open-Source Software for two reasons, I love Linux and I want this to be available for everyone and I don’t want a paywall stopping someone from creating amazing things.
If you find any material, presented on this channel, useful, please consider sharing it and supporting rebelScience project. Any and all donations will be used for creating new content (articles, videos, chat/forum administration) and covering costs of web hosting. But no matter what, all of my educational content will always stay open and free.
Ways to support: rebelscience.club/cryptocurrency-donations/
Telegram: t.me/biocodex
Matrix: #biotechdna:matrix.org
E-Mail: rebcoder@pm.me
In my work I only use 100% Open-Source Software for two reasons, I love Linux and I want this to be available for everyone and I don’t want a paywall stopping someone from creating amazing things.
If you find any material, presented on this channel, useful, please consider sharing it and supporting rebelScience project. Any and all donations will be used for creating new content (articles, videos, chat/forum administration) and covering costs of web hosting. But no matter what, all of my educational content will always stay open and free.
Ways to support: rebelscience.club/cryptocurrency-donations/
Telegram: t.me/biocodex
Matrix: #biotechdna:matrix.org
E-Mail: rebcoder@pm.me
Genome Toolkit. Part 3: building statistical data (k-mer frequency)
Biologists can use k-mer analysis to identify conserved sequences across different species. This can help them to understand the evolutionary relationships between different organisms and identify potentially functional sequences that have been conserved over time. In this video, we will add such an algorithm to our Genome Toolkit.
Article version: rebelscience.club/2022/12/genome-toolkit-part-3-building-statistical-data-k-mer-frequency/
GitLab: gitlab.com/RebelCoder/genome-toolkit
[===============================]
Ways to support rebelScience: rebelscience.club/cryptocurrency-donations/
Join the community:
Telegram: t.me/biocodex
Matrix: bit.ly/3rFaS9Z
Social media:
Twitter: rebelCode...
Article version: rebelscience.club/2022/12/genome-toolkit-part-3-building-statistical-data-k-mer-frequency/
GitLab: gitlab.com/RebelCoder/genome-toolkit
[===============================]
Ways to support rebelScience: rebelscience.club/cryptocurrency-donations/
Join the community:
Telegram: t.me/biocodex
Matrix: bit.ly/3rFaS9Z
Social media:
Twitter: rebelCode...
Просмотров: 3 047
Видео
Bioinformatics Tips & Tricks: A faster search for patterns (loop, list, regexp)
Просмотров 1,6 тыс.Год назад
In this video, we are going to take a look at one of the algorithms we wrote in Genome Toolkit series, Part 2, and attempt to optimize it. We will also discuss the approach a beginner in Python can take to learn how to write better, faster, and more Pythonic code. We will finish by measuring execution speed of all of our solutions, and discuss if it even is worth your time, to optimize your cod...
Genome Toolkit. Part 2.1: identifying, fixing, and testing a bug
Просмотров 1,5 тыс.Год назад
In the previous article (Part 2 here), we wrote our first Genome Toolkit algorithm. Even though it was a very simple algorithm to help us search for repeating patterns, (k-mers in DNA/Genome sequences), and it seemed to work correctly, we actually had a bug in it. Let’s take a look at it, and how we can fix it. Article version: rebelscience.club/2022/11/genome-toolkit-part-2-1-identifying-fixin...
Genome Toolkit. Part 2: in search of patterns
Просмотров 2,1 тыс.Год назад
Our first function will count repeating patterns, also known as k-mers, in a sequence. This is a very basic, but still useful algorithm for biologists. It can be used as one of the steps in pattern search in genomes. Article version: rebelscience.club/2022/10/genome-toolkit-part-2-in-search-of-patterns/ GitLab: gitlab.com/RebelCoder/genome-toolkit [ ] If you found this video useful, please cons...
Genome Toolkit. Part 1: project setup
Просмотров 3 тыс.Год назад
Welcome to the new series, called “Genome Toolkit”. In this series, we will write a set of tools, that will help us find and build statistical data around any DNA, RNA, and Protein sequences. We will start by looking at the basic needs of any biologist, and write algorithms around their needs. The main goal of this series is to build a set of algorithms, and wrap them into a usable bioinformati...
rebelScience: Forum & Matrix Space
Просмотров 3272 года назад
Bioinformatics Forum and Matrix Space announcement & introduction video. I am starting a rebelScience Bioinformatics forum. A lot of subscribers and chat members are interested in collaborating on a variety of projects, solving Rosalind challenges together, and just having structured and constructive discussions. This forum will be private, and invite-only for some time, until we build a small ...
rebelScience: Channel Update #1
Просмотров 1,4 тыс.2 года назад
This is a quick channel update. It has been a while since the last video on this channel, and we have just reached 9000 subscribers. I want to say "thank you" to everyone who helped this channel to grow, by subscribing, watching and commenting. In this video, I want to provide a quick channel update. [ ] Ways to support: rebelscience.club/cryptocurrency-donations/ Telegram: t.me/biocodex Twitte...
Bioinformatics London Meetup. Data-driven drug discovery & 3D genetics. [29.11.2020]
Просмотров 1,6 тыс.3 года назад
Speakers: * Amir Feizi (Bioinformatics Director - OMass Therapeutics) on “Data-driven drug discovery in biotech and pharma” Amir Feizi holds a Masters’ degree in bioinformatics and received his PhD in systems biology from Chalmers University of Technology, Sweden, under the mentorship of Jens Nielsen (CEO of the BioInnovation Institute, Copenhagen). He worked on translational cancer genomics pl...
Bioinformatics London Meetup. Part 2. [01.10.2020]
Просмотров 8233 года назад
London Bioinformatics Meetup. Title: How Computer Vision is being used to help Parkinson's Disease patients Abstract: Computer vision applications have the potential to transform how healthcare practitioners work. One such application is KELVIN-PD, which precisely measures human movement, thus allowing clinicians to get a better understanding of how Parkinson's disease patients are reacting to ...
Bioinformatics Tips & Tricks: Hamming Distance
Просмотров 4,8 тыс.4 года назад
In this video, we solve Hamming Distance in three different ways. #Bioinformatics #Python [ Video Notes/Links ] GitLab Link: gitlab.com/RebelCoder/bioinformatics_tips_tricks [ Community chat/communication ] Website: rebelscience.club/ Telegram (Chat): t.me/biocodex Telegram (News): t.me/biocodex_news Matrix: biotechdna:matrix.org Twitter: rebelCoderRU Mastodon: mastodon.social/@Rebe...
Bioinformatics Tools Programming in Python with Qt. Part 2.
Просмотров 1,4 тыс.4 года назад
In this quick video, we create a file structure for our project, add a DNAEngine class and a 'main' function. #Bioinformatics #Python #Qt #PyQt [ Video Notes/Links ] Article version: rebelscience.club/2020/06/part-2-dna-engine-structure-dna-toolkit-import/ Recommended Rust programming books: Mastering GUI Programming with Python: Develop impressive cross-platform GUI applications with PyQt by A...
From Python to Rust. Part 3: A Dictionary and a HashMap.
Просмотров 3,2 тыс.4 года назад
In this video, we look at Python dictionary and Rust HashMap and implement a DNA reverse complement function in both. #Bioinformatics #Python #Rust [ Video Notes/Links ] Article version: rebelscience.club/2020/06/from-python-to-rust-part-3/ Rust HashMap video #1: ruclips.net/video/sTK8fagTsMk/видео.html Rust HashMap video #2: ruclips.net/video/ic9WEuto-gE/видео.html .iter() - ibit.ly/wYNW .copi...
Data and Code Sharing in Bioinformatics: From Bermuda to Toronto to Your Laptop
Просмотров 1 тыс.4 года назад
Talk by Professor Victoria Stodden, Department of Statistics, Columbia University. The talk was given at UC Berkeley. Large-scale sequencing projects paved the way for the adoption of pioneering open data policies, making bioinformatics one the leading fields for data availability and access. In this talk I will trace the history of open data in -omics based research, and discuss how open code ...
Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase
Просмотров 9784 года назад
Talk by Chris Lee, UCLA. Presented at Python for Scientific Computing Conference held August 18-23, 2009 at CalTech in Pasadena CA. Information about the conference is at: conference.scipy.org Original publication date: 2009 About: This is a public, archive.org/ sourced video, not available on RUclips. Sound has been 'cleaned' (noise reduction has been performed). Source: archive.org/details/sc...
Bioinformatics Tools Programming in Python with Qt. Part 1.
Просмотров 3,8 тыс.4 года назад
We start by setting up PyQt and a virtual environment for our project and run a Test App. After that, we will generate our first UI file and load it into our project. #Bioinformatics #Python #Qt #PyQt [ Video Notes/Links ] Article version: rebelscience.club/2020/05/bioinformatics-tools-programming-in-python-with-qt-part-1/ PyQT5 Designer installation and use on Windows Video: ruclips.net/video/...
From Python to Rust. Part 2: Strings, Functions & Crates/Modules.
Просмотров 3,4 тыс.4 года назад
From Python to Rust. Part 2: Strings, Functions & Crates/Modules.
Bioinformatics in Python: DNA Toolkit. Part 9: RNA, Helper functions
Просмотров 4,9 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 9: RNA, Helper functions
Bioinformatics in Python: DNA Toolkit. Part 8.2: Code refactoring into a bio_seq class
Просмотров 4,6 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 8.2: Code refactoring into a bio_seq class
Bioinformatics in Python: DNA Toolkit. Part 8.1: Code refactoring into a bio_seq class
Просмотров 5 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 8.1: Code refactoring into a bio_seq class
Bioinformatics in Python: DNA Toolkit. Part 7: A search for a real protein from NCBI database
Просмотров 7 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 7: A search for a real protein from NCBI database
Bioinformatics in Python: DNA Toolkit. Part 6: Protein search in a reading frame
Просмотров 8 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 6: Protein search in a reading frame
Rosalind Problems: Fibonacci, Rabbits and Recurrence Relations
Просмотров 8 тыс.4 года назад
Rosalind Problems: Fibonacci, Rabbits and Recurrence Relations
Bioinformatics in Python: DNA Toolkit. Part 5: Open Reading Frames
Просмотров 12 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 5: Open Reading Frames
Bioinformatics Tips & Tricks: Development Tools Setup
Просмотров 8 тыс.4 года назад
Bioinformatics Tips & Tricks: Development Tools Setup
Bioinformatics in Python: DNA Toolkit. Part 4: Translation, Codon Usage
Просмотров 13 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 4: Translation, Codon Usage
Rosalind Problems: GC Content, FASTA File Format, Data Processing
Просмотров 13 тыс.4 года назад
Rosalind Problems: GC Content, FASTA File Format, Data Processing
Bioinformatics in Python: DNA Toolkit. Part 3: GC Content Calculation
Просмотров 15 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 3: GC Content Calculation
Rosalind Problems: Transcription and Reverse Complement
Просмотров 8 тыс.4 года назад
Rosalind Problems: Transcription and Reverse Complement
Bioinformatics in Python: DNA Toolkit. Part 2: Transcription, Reverse Complement
Просмотров 25 тыс.4 года назад
Bioinformatics in Python: DNA Toolkit. Part 2: Transcription, Reverse Complement
this is one of the most information rich tutorial channels that I've ever seen
Thank you so much! Glad you find the content valuable!
Is test_dno = bio_seq() called 'assigning an import to a variable' or 'assigning a class to a variable?' or, more generally: what is it called?
Hey! So, bio_seq is a class. The process of creating a variable and assigning an instance of a class to it in Python is called: Instantiation So this: test_dna = bio_seq() is Instantiation of a class bio_seq() is calling the constructor of the bio_seq class, which creates a new instance of that class. test_dna is the variable that holds a reference to this new instance I hope that makes sense.
@@rebelScience great answer!
Currently running all these code in a decentralised Cartesi VM for a side project. Thanks for these videos
Sounds amazing. I know the Cartesi Blockchain project.
@@rebelScienceI will share with you when I am done next week
junior bioengineer here thank u so much u helped me a lot <3
Thank you very much buddy! I'm a first year Biotech student and I needed this badly 🙏
Nice video man but please, I thought the other way for summing odd numbers was range(start, end, count)🥺
Thank you!
My brother, dictionaries have a values method so you don't have to write that long list comprehension
def hamming_distance(string1, string2): return sum( [ string1[i] != string2[i] for i in range(len(string1)) if len(string1)==len(string2)])
I get the error: no module named DNAToolkit - I tried installing the DNA toolkit from PIP, and I thought it would work, but still giving me the same error. I copied the code, from what I could tell, exactly. Any thoughts?
am i the only one who tried all the possible solutions but the script either give me a 100% if the string only contains G and C or 0% if else !
Hello, i have this problem, it gave me this output {'A': 16, 'C': 12, 'T': 6, 'G': 16} while I entered the dictionary in this order {"A": 0, "C": 0, "G": 0, "T": 0} why it switches the T and the G order in the output ?? please help me cuz I'm stuck here thanks
I am unable to get correct answers all my answers are wrong. Please help.
please share the gitlab link.
Wow all in one channel its pretty cool ❤
Excelent videos, i really apretiate that you give us this quality content, as a biology student who is also learning to code you have showed me a part of biology that i never knew it existed, thank you
Haven't reached this video yet, but seeing as you said this would be a longer series than DNA toolkit, I presume you're on some sort of hiatus. Just here to say your videos are a great benefit to all of us watching, hope you resume this series sometime soon.
Hello, thank you for sharing these intriguing videos. I have a question regarding copying the whole fasta code into a unique single line. Could you please explain how that process works?
Or How can I use an external file to upload my sequences?
what is this interface in which youre working ? thanks
Do you mean the code editor? VSCodium. I have a video about it. And I talk about it in my Intro video.
@@rebelScience You recommend it for Phtyon language? thanks
Thank you for this series, it was ready easy to follow along!
Glad it was helpful!
impossible to watch, f**k yt
Please do more useful information about bioinformatics
I want to work in the longevity and anti aging field, this will be a useful resource. Thanks
jesus, i'm in love with this playlist. thank you so much <3
Glad you enjoy it!
Hi, I can't find the third video of the series Bioinformatics Tools Programming in Python with Qt. Have you deleted it?
I'm studying with your videos. but when I print result, It show different result when I runned. If the random result tart from G, dictionry's result shows also G. Is it OK? If I use join list comprehension, how could I know which one is A or G or C or T ?? If I like to make a dic list start from A, C, G and T , how to make a code...?
also... If i "print(' '.join([str(val) for key, val in result.items()]))" this one, when I print dic. it has blank value and key, should I '' (without black), instead ' '(with black) ? but If I use '' , the print resule show 20121721 no 20 12 17 21... I couldn't find out what is different with yours..
thank you sir
thank you
I forgot to remove the ''>" initially and it kept getting marked incorrect on Rosalind. Thanks for pointing this out!
On the Rosalind channel, they had really elegant python solutions in the comments after the exercise. This one was only one line of code to accomplish this task. Thanks for introducing us to this site! print(list(DNAstring.count(nuc) for nuc in 'ACGT'))
thank you very much
thank you sir
hello thumbs up to all the dna toolkits tutorials, I'm about to create a virtual environment but got stuck. I need help. I want to join the online forum but unfortunately it requires an invite code to sign up
Thank you, I like the pace of the teaching and the relevant examples used for bioinformatics.
9:11 absolutely... I never liked programming, and always hated the stupid programs my instructors would usually give. The truth is that I just never saw much of an important problem worth the efforts of coding, that's challenging and rewarding
Very cool videos. Thank you for making and sharing them. Look forward to the next one in this series.
nice!
Actually, I think in the section of working with files, we add start = 1 in enumerare function, this is much better to understand.
I love your veido, it's amazing, especially rosalind, learning python to solve interesting and practical question is meaningful.
How do you do a bulk rename at 6:59? edit: Okay I see you do it by right clicking on the word you wish to rename and hitting rename symbol.
Thank you for making this video, I have been wanting to start using Visual Studio. So far, I have only used PyCharm. I am very much a beginner with programming so help with set up is very much appreciated.
Is Python used for Lipidomics or metabolomics data analysis?
Is this tutorial closed??
I just want to share some notes I have. There is probably a more efficient way for this to be done, but I figured out a way to do transcription and make a reverse complement for a given DNA sequence. Transcription for a given sequence: main: # DNA Toolset/Code testing file from DNAToolkit import * #this line here is where to put the code to be transcriped givenDNAStr = "AGTC" DNAStr = validateSeq(givenDNAStr) print(transcription(DNAStr)) DNATool kit: Nucleotides = ["A", "C", "G", "T"] # Check the sequence to make sure it is a DNA string def validateSeq(dna_Seq): tmpseq = dna_Seq.upper() for nuc in tmpseq: if nuc not in Nucleotides: return False return tmpseq def transcription(seq): # DNA to RNA a process known as transcription return seq.replace("T", "U") For a reverse complement of a given DNA sequence: main: # DNA Toolset/Code testing file from DNAToolkit import * # insert a desired sequence for complement: givenDNAStr = 'AGTC' DNAStr = validateSeq(givenDNAStr) print(f' DNA sequence: {DNAStr} ') print(f'Complementary DNA sequence: {reverse_complement(DNAStr)} ') DNATool kit: Nucleotides = ["A", "C", "G", "T"] DNA_ReverseComplement = {'A': 'T', 'T': 'A', 'G': 'C', 'C': "G"} # I am not sure what this line of code is doing, but the results won't run in the terminal without it def validateSeq(dna_Seq): tmpseq = dna_Seq.upper() for nuc in tmpseq: if nuc not in Nucleotides: return False return tmpseq def reverse_complement(seq): return ''.join([DNA_ReverseComplement[nuc] for nuc in seq])
Great video. Thanks. For this function, I tried iterating the aa sequence from the end. Mark the current "_" as an end. Append every seq with newly found “M” to proteins[]. It seems less time and space used.
for the line rfs = gen_reading_frames(seq[startRead: endRead]), I get startRead, endRead not defined I tried startReadPos, endReadPos but that didn't work either. Are these built in functions from a module I am missing or am I just being an idiot?
Also thank you for all your wonderful content
Hello, thanks for this course about Bioinformatics. I noticed that only one strand from DNA is transcribed and translated, but I suppose your video with the both strands is only included in the function for additional information? Best!
Good tutorial, I wanted to ask if I wanted to build a project that does DNA alignment, do you have any recommendations on tutorials or step by steps? (Ideally I would prefer a tutorial of yours - enjoyed your videos)
Hey! There will be a sequence alignment in the Genome Toolkit, but in a few videos. No ETA at the moment, unfortunately.
what ide is this?
Hey! You should start with the Introduction video, where I explain what you need to work with this series of video, including the code editor. I also have a video of how to set it up.
You explain your codes and concepts very well. Your DNA and genome toolkit videos are a great introduction in Python for a biologist!