12/15/2023 Bioinformatics

Guide
Ahmed Usama Farahat

Ahmed Usama
01013387168
Coding:
Python:
Basic Python:
https://youtube.com/playlist?list=PL2R8FcAkoPrU_X54uZDvaIKJoGRlz8Zku&si=v9JT-
mflFVWvlb3J
GUI in Python:
https://youtube.com/playlist?list=PLCC34OHNcOtoC6GglhF3ncJ5rLwQrLGnV&si=Aph-
iyRulZXv19jC
Biopython:
https://youtube.com/playlist?list=PLhYDP66xNTKRdtUM8ekEmq1fC0mosXrgn&si=zrrqQ7k4
RBL0Rymm
Advanced Biopython:
https://youtube.com/playlist?list=PLNj5Z_OpbXrIRz6H8iaBfVJyIkWplNb1D&si=XO82npFBv
BXJbGIf

R Studio:
Part 1
https://youtube.com/playlist?list=PLC4LFcwOQGSEba8Uha5Hp7WBzU2T_RT_8&si=Th26xE
oNLR15ksOb
Part 2:
https://youtube.com/playlist?list=PLC4LFcwOQGSGg3YPtoTVAX1znRblEo-
9j&si=C5JGU4PbsSkFjepU
Part 3:
https://youtube.com/playlist?list=PLC4LFcwOQGSFqZgpvT76obvkph0SADHBk&si=loAwGU
cbjtaSlwSe
Part 4:
https://youtube.com/playlist?list=PLC4LFcwOQGSGTydn4NPPr76Pz2i-
Xa2sX&si=rnjqlh1OE4g7SnCw
Part 5:
https://youtube.com/playlist?list=PLC4LFcwOQGSHbmds9_2ue9Z5kJY9hG71n&si=gr6xdmqG
cbSltDfm
Part 6:
https://youtube.com/playlist?list=PLC4LFcwOQGSHi1KVjb_8WEdsCV36hLSLk&si=ZSWBq
GrSV8qYBegS
Data Science with R:
https://www.simplilearn.com/big-data-and-analytics/data-scientist-certification-sas-r-excel-
training

Matlab:
https://youtu.be/T_ekAD7U-wU?si=zufWcZVow78eEsZo

1|Page
Linux:
https://youtu.be/sWbUDq4S6Y8?si=Rsh7yftW74ZjLwQn

Bash Scripting:
https://youtube.com/playlist?list=PLT98CRl2KxKGj-VKtApD8-
zCqSaN2mD4w&si=i43uA5KIxa-Wt_G3

Machine Learning:
https://youtube.com/playlist?list=PLoROMvodv4rMiGQp3WXShtMGgzqpfVfbU&si=FG8t3vaq
MVtfMcrD

Data Analysis:
https://youtu.be/r-uOLxNrNk8?si=PSv0w1r3Ayo_2XZb

Biostatistics:
Principles, Statistical and Computational Tools for Reproducible Data Science:
https://www.edx.org/learn/data-science/harvard-university-principles-statistical-and-
computational-tools-for-reproducible-data-science
Fundamentals of Statistics:
https://www.edx.org/learn/statistics/massachusetts-institute-of-technology-fundamentals-of-
statistics
Probability:
https://www.edx.org/course/data-science-probability
Statistics and R:
https://pll.harvard.edu/course/statistics-and-r
Linear Regression:
https://pll.harvard.edu/course/data-science-linear-regression

Bioinformatics Tools:
AlphaFold:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
Blast:
https://blast.ncbi.nlm.nih.gov/Blast.cgi
Reverse Complement:
https://www.bioinformatics.org/sms/rev_comp.html
ORFfinder:
https://www.ncbi.nlm.nih.gov/orffinder/

2|Page
Qpromoter:
https://qpromoters.com/
RNAFold:
https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=http://rna.tbi.univie.
ac.at/cgi-
bin/RNAWebSuite/RNAfold.cgi&ved=2ahUKEwjE24Xt5JGDAxWkUqQEHVHeAhoQFnoEC
CsQAQ&usg=AOvVaw3m8YXdJH8MbG2FNxtpuNuK
RFdiffusion:
https://colab.research.google.com/github/sokrypton/ColabDesign/blob/v1.1.1/rf/examples/diffusi
on.ipynb
Expasy:
https://www.expasy.org/
Galaxy:
https://galaxyproject.org/events/2021-02-smorgasbord/

Mathematics:
Calculus:
https://youtube.com/playlist?list=PL590CCC2BC5AF3BC1&si=ZnQLJhDrvd15BiUw

https://youtube.com/playlist?list=PL4C4C8A7D06566F38&si=4CXR9QFjVTJGbyZ6
Linear Algebra:
https://youtube.com/playlist?list=PL221E2BBF13BECF6C&si=1yAqAd_dezWWCrKi
Ordinary Differential Equations:
https://youtube.com/playlist?list=PLUl4u3cNGP63oTpyxCMLKt_JmB0WtSZfG&si=Vs-
IcgDO9IRVeaWS

Skills:
Differential Gene Expression:
https://youtube.com/playlist?list=PLJefJsd1yfhbIhblS-
85alaFsPdU00DaA&si=qUdZ0dXs3H7UzgNx
Single Cell Seq:
https://youtube.com/playlist?list=PLJefJsd1yfhagnkss5B1YCsHaH0GWQfFT&si=UbxMjDu3d_
e6DXhd
RNA-seq:
https://youtube.com/playlist?list=PLJefJsd1yfhbIhblS-
85alaFsPdU00DaA&si=qUdZ0dXs3H7UzgNx
PyMol:

3|Page
https://youtube.com/playlist?list=PLZANrlj_zCh9A2G8RdFUnxqojGukq49Q_&si=thga63Jc1HI
sfSYI
Chimera:
https://youtube.com/playlist?list=PLHib7JgKNUUeTZONxd0h0WBiZzAJmXmva&si=tTzt6lfl6
8sa0g5g
Homology Modeling:
https://youtube.com/playlist?list=PLoCxWrRWjqB3A1Jhs_HSbED9Z3ViH--
bI&si=UbRHFrwO3_FPa2ZC
Molecular Dynamics:
https://youtube.com/playlist?list=PL1Bs8qNrKtJ6E0RC7UpHStTZElxJZhIXa&si=OrsqQHViL_
wew0_j
AlphaFold:
https://youtu.be/UqeQfRDA8Yk?si=HLgQxfLwbtbmvC_O
Molecular Docking:
https://youtu.be/2ewpDYW081Y?si=SNFralpNgU_4Dldb
Virtual Screening:
https://youtu.be/tFFxNTvvoJI?si=vMJJkW-8rrXVgnHo

Courses:
File Formats:
https://youtube.com/playlist?list=PLJefJsd1yfhbSiT2Yc0CBaj9WonFDXGsU&si=V-
1OWqjqU7rOvuPW
Bioinformatics:
https://www.coursera.org/specializations/bioinformatics
System Biology:
https://www.coursera.org/specializations/systems-biology
Computational Neuroscience:
https://www.coursera.org/learn/computational-neuroscience
Organizations:
BioNome:
https://www.linkedin.com/company/bionome/
NyBerman:
https://www.linkedin.com/showcase/nyberman/
Neuromatch:
https://www.linkedin.com/posts/arabs-in-neuroscience-ain_new-volunteer-opportunities-we-are-
activity-7136003037524873220-nUYZ?utm_source=share&utm_medium=member_android
Plasma:

4|Page
https://www.facebook.com/Plasma.egy1?mibextid=eHce3h
Biosyn:
https://www.facebook.com/profile.php?id=100089766484212&mibextid=eHce3h

Online Non-degree bachelor in Bioinformatics & computational

Biology:
https://m.facebook.com/story.php?story_fbid=pfbid0WRtG1jh5JbASKrBAcMoKVxBxz192ZiAj
m6TYV4sUNgQxk6zeDfiW8XCnHTqfX28Kl&id=1193316792&mibextid=Nif5oz

5|Page