Homework 2
Error propagation
Homework 1
Handle large numbers
History of Molecular Evolution
In this course we discuss the history of ideas about evolution, with emphasis on the molecular aspects.
Methodology of Scientific Research
This course teaches the Scientific Method, its history and its applications. We discuss how to observe, measure and model reality to understand it.
Our paper in the news around the world
After a long process, the work done with Dr. Emrah Kırdök, Dr. Anders Götherström and many other researchers has been published in a top-notch journal, and it has got a lot of press around the world.
Homework 8
Design primers for finding a gene in a metagenomic sample.
Homework 7
Reconstruct phylogenetic trees.
Homework 6
Buid trees.
Homework 5
Find proteins similar to human hemoglobin.
Homework 2
Calculate p-values on simulated data. ANOVA and t Student test.
Homework 4
Calculate global and semi global Levenstein distances between sequences.
Homework 3
How would you calculate the Hamming distance between genetic codes?
Homework 2
Read about genetic codes.
Homework 1
Practice creating NCBI Entrez queries.
Bioinformatics course
This course teach how to interpret and understand the results of bioinformatic analyses. Even if they do not use the tools, all molecular biologists need to understand the meaning of bioinformatics results. It is important to speak the same language, and be aware of the key aspects that can lead to the experiment's success or failure.
Systems Biology
Systems Biology is a systemic approach to understand the biological phenomena that occurs inside a cell at the molecular level. This course is an introduction to the theoretical tools that are used to understand the emerging behavior of complex biological networks.
Homework 9
Test your probabilistic skills.
Homework 8
Test your logic skills.
Homework 7
Making a house fly using balloons.
Homework 6
What is the weight of this ferry?
Homework 5
Practice interval arithmetic
Homework 4
Handle large numbers
Homework 3
Ask good questions
Homework 2
Is the Earth flat?
Homework 1
What is Science, according to you?
Methodology of Scientific Research
This course teaches the Scientific Method, its history and its applications. We discuss how to observe, measure and model reality to understand it.
DNA melting temperature
Energy, entropy and thermodynamics
Homework 9
This week we practice using Galaxy to analyze RNAseq data.
Homework 8
This week we practice drawing trees and doing multiple alignments.
Homework 7
Explain probabilities, draw trees.
Homework 6
Better searches, and comparing bacterial strains.
Evaluation of Midterm exam
Please check your Midterm grades and tell me id there is anything wrong
8. Looking for a professor
Here the key point is to describe a good query. It should include France[Affiliation], review[Publication Type], 2017:3000[Date - Publication], and something about metagenomics. Searching in all fields is a bad idea, since it may match a comment. Searching in the title is good, but it may miss some cases. The best query term, in my opinion, is metagenomics[MeSH Terms].
7. Average Nucleotide Identity
Student 1 50
6. Word Size
For a fast search we use a large word size, which may miss some results. To find more results, i.e. to be more sensitive, we use a small word size.
5. Existence/extension?
The biological reason for affine gaps is that indel initiation is hard, but once it exist, extensions are easy. In other words, nature prefer few long gaps instead of many short ones.
4. How BLAST works?
The key word here is index. BLAST uses an index to search for partial matches, or seeds, that are later extended using the local alignment matrix.
3. Algorithm v/s Heuristics
An algorithm is a protocol to find the answer to a specific question. Sometimes they take a very long time to finish, so instead we ask a different (but similar) question that can be answered in a shorter time. This is an heuristic.
2. Entrez query
The key idea here is that [orgn:exp] will match entries associated with the given taxon and entries associated with taxa located under the given taxon in the taxonomy tree. In this case the taxon is a species, and the expanded taxa are subspecies and strains.
1. Taxon
A taxon is any node in the taxonomy tree. This is the core idea.
Homework 5
Prepare for the midterm exam.
Homework 4
Learning Excel and factorials
Bioinformatics 2022
This course teach how to interpret and understand the results of bioinformatic analyses. Even if they do not use the tools, all molecular biologists need to understand the meaning of bioinformatics results. It is important to speak the same language, and be aware of the key aspects that can lead to the experiment's success or failure.
Homework 3
Prepare dot plots, calculate Hamming distance.
Homework 2
Read about genetic codes
Homework 1
Practice creating NCBI Entrez queries
Methodology of Scientific Research
This course focus in theoretical and practical aspects of doing science. In particular we learn how to design good experiments that can create high-impact knowledge.
Handling thesis drafts
If you are doing your thesis under my supervision, then you need to read this article. It describes how we interact using online tools.
Rules for writing
Scientists are writers. Papers, reports, projects, and so on. It is important to write clearly to be understood. If you write in manuscript, you need to use a good calligraphy. There are also rules for typing a text in the computer. Here are these basic rules.
All homework for the bioinformatics course
In case you have forgotten, here is a list of all that you must deliver.
Bibliography for Bioinformatics
These are some of the papers we want to read and understand during this semester. The most important ones are marked in bold face. Start by reading those ones.
Systems Biology
Systems Biology is a systemic approach to understand the biological phenomena that occurs inside a cell at the molecular level. This course is an introduction to the theoretical tools that are used to understand the emerging behavior of complex biological networks.
Bioinformatics 2021
This course teach how to interpret and understand the results of bioinformatic analyses. Even if they do not use the tools, all molecular biologists need to understand the meaning of bioinformatics results. It is important to speak the same language, and be aware of the key aspects that can lead to the experiment's success or failure.
Homework 9
We cannot predict the future, but we can make educated guesses. Practice educating your guesses.
Homework 8
What will be your score in the exam? Use simulation to see what will probably happen.
Homework 7
Practice of Montecarlo method. Simulate “complex” random systems by decomposing them into simpler ones.
Some answers to Homework 5
Some students have been generous and shared their answers to homework – after the deadline, of course. Here you can see their answers and some of my comments.
Some answers to Homework 6
Some students have been generous and shared their answers to homework – after the deadline, of course. Here you can see their answers and some of my comments.
Homework 6
Simulate a predator-pray system, using Lotka-Volterra model.
Computing in Molecular Biology 2
Introduction to Computational and Quantitative Thinking. Systems to understand the universe, and simulations to predict their consequences.
Homework 5
Count rabbits with recursive functions and with a loop.
Homework 4
Practice writing functions, for loops and conditional blocks.
Homework 3
Practice writing functions and applying them to several elements of a list.
Calculating π as Archimedes did
Every 14 of March, mathematical inclined people around the world publishes articles about π, circles and diameters. Here we use the tools developed in previous posts to calculate some digits of π.
The secret number, the golden number, and the Babylonian method to find them
Now that we know how to calculate numbers with a lot of decimals, let's look for the number that Pythagoras does not want you to know, and for the number made of gold.
Ten thousand digits of 𝑒
Your computer is better than your dad's computer. It can easily do things that old computers had hard time doing. We just need to think it well and explain the steps one by one.
Homework 2
Teach the computer how to write the flag of Turkey.
Homework 1
Write to learn.
Methodology of Scientific Research
This course focus in theoretical and practical aspects of doing science. In particular we learn how to design good experiments that can create high-impact knowledge. This year we will focus on gene expression experiments.
Final Exam answers received
Do you want to verify that I received your answer? Do you want to check that I got the correct file? Here you have the summary of all files received until 12:42, February 6.
Homework: Genome assemblers
There are several free DNA assemblers available on the web. We need to use some of them. Your homework is to find them, and identify its primary characteristics.
Homework 5
Practice for final exam. Plots and linear models.
Homework 4
Practice for midterm exam. Tidying up real-life data.
Computing in Molecular Biology 1
How to
Homework 3
Practice for midterm exam. Vectors and indices, again.
Homework 2
Practice for midterm exam. Vectors, indices, and general ideas about using R.
Bioinformatics 2020
This course teach how to interpret and understand the results of bioinformatic analyses. Even if they do not use the tools, all molecular biologists need to understand the meaning of bioinformatics results. It is important to speak the same language, and be aware of the key aspects that can lead to the experiment's success or failure.
Makeup Exam answers received so far
Do you want to verify that I received your answer? Do you want to check that I got the correct file? Here you have the summary of all files received until 17:04, August 16.
Comments on Midterm Exam, part 2
This is the second part of three posts explaining some ways to answer the midterm exam.
Comments on Midterm Exam, part 1
This is the first part of three posts explaining some ways to answer the midterm exam. Check you answers.
Comments on Final Exam, part 2
This is the second part explaining some ways to answer and some common mistakes. Read it and ask questions in the comments section.
Comments on Final Exam, part 1
Many students asked about the answers to out Final Exam. This is the first part of two posts explaining some ways to answer and some common mistakes. Read it and ask questions in the comments section.
How to make a lot of sums
This is an issue that I see again and again in your questions, so I will explain it in a different way.
Fixing Errors in the Exam
There are two error in the Exam questions. Read here to avoid confusion.
Comments on Question 2.4 – Final Exam
A new explanation of question 2.4, and some examples.
Final Exam answers received so far
Do you want to verify that I received your answer? Do you want to check that I got the correct file? Here you have the summary of all files received until 09:21, July 4.
Midterm answers received so far
Do you want to verify that I received your answer? Do you want to check that I got the correct file? Here you have the summary of all files received until 18:43, June 7.
I'm on Chilean TV!
Among the several shows in Chilean TV, there is one about Chilean expats. It is called “Siempre hay un Chileno” (that is “There is always a Chilean”). The name comes from the idea that, wherever in the world you go, there will alway be a Chilean migrant.
Wizardry
Freefall by Mark Stanley, October 18, 1999
Linear models for microarray analysis
A gene expression experiment measures messenger RNA concentrations under a specific growth condition. We would like to know how does a gene concentration change when conditions change. But our measurements mix real gene expression and noise. How can we find separate noise and signal?
La Biblioteca de Babel de Borges
How many books? How many planets?
Solving Triangle Peg Puzzle with Unix command line tools
Matt Parker's 5th Puzzle
Linear models with categorical factors
Linear models allow us to predict from experimental data, and define confidence intervals for these predictions. Moreover, the coefficients of the linear model reveal useful information, with their corresponding confidence intervals. In this article we explore the case when some of the independent variables are not numeric but instead are in a nominal scale.
Homework 9
Explain in English what are the parts of each of these systems, and what do you think will be the systems' behavior.
Homework 8
Explain in English what will the system do.
An easy way to transform your R script into a nice report
Let’s say we have written an R script and we want to include some comments about it. For example, we want to discuss the meaning of the results. It is easy to make a report from your R script, with the simple changes we discuss here.
Application: Uncertainty in Linear models
Beyond making predictions, linear models allow us to measure values that are hidden under a mountain of data. Learn how to measure these values and determine their confidence intervals.
Experiment: measuring the speed of sound
It is not hard or expensive to measure the speed of sound. But, what are the margins of error?
Uncertainty in Linear Models
When we can assume that real values follow a straight line, we can reduce the uncertainty. Thus, we can predict the number of COVID-19 cases, and see if health-care decisions are effective or not.
How to solve hard problems
People are asking “How can I solve the homework? It is too hard”. Here are some steps that may help you.
Homework 7
Keep your mind sharp. Prepare for the next stage of online learning. Learn how to find biological meaning in genomic data —codon usage, GC-skew— using basic programming tools.
Application: Evaluating Statistical Uncertainty
Measuring the same value several times may give different results. The real value is somewhere in a confidence interval. To find such interval we need to evaluate the statistical uncertainty.
Estimating Statistical Uncertainty
Every time we measure, we get a different number. How can we extract meaningful information from noisy data? How much information can we extract? Classical statistics gives an answer to these questions.
Homework 6
Exercise your brain for the midterms. Using the computer to handle DNA data safely at home.
Hard problems
Some students argue that the exercise “find the largest value” is too hard. This raises the question “What do we mean by hard problem”? The answer teach us important things about life, the universe, and everything.
Comments on Homework 5
Several students have delivered their homework. Some are good, some are worth looking at them. I want to share them with everybody, so everybody can learn.
Three weeks of no-holiday
Universities in Turkey are closed for at least three weeks, as a way to contain the spread of Covid-19. It is easy to fall into the trap of doing “nothing”, watching TV, and read social media. But easy is not wise. Use your time wisely.
Homework 5
Practice of functions, for DNA analysis and for fun. Getting ready for the midterms.
Homework 4
We jump into functions, the key piece for the rest of the course. We start with one question in four versions. If you look carefully, they are all essentially the same question, so if you solve the first one, the rest should be easy.
Homework 3
This week we will practice decomposition, pattern matching, and algorithm design by creating an R script to draw simple figures. And we learn the discipline to deliver homework always on time, even if it is not ready.
Recommended Podcast
One of the things I do to not get bored in public transport is to listen podcasts. I have several favorites, but that is a story for another day. Today I want to recommend two recent episodes of one of my favorite podcasts.
Homework 2
Peer-review of first exercise. Learn to recognize good and bad decompositions. Learn to give feedback. Train to be a referee.
Homework 1
Take a complex drawing and decompose it in many smaller parts
Methodology of Scientific Research
What is the value of Science? In this course we will discuss why do we need Science, how Science improves people’s lives and how to do it better.
Computing in Molecular Biology 2
This course is an introduction to Computational Thinking. We will use the tools we learned in the previous course and apply them to model and simulate scientific experiments as a way to understand them.
Homework 4 (Practical)
Preparation for final exam.
Homework 7
Exam Rehearsal.
Homework 6
Subsets and linear models.
Homework 5
Scatter plots, choose colors, size, titles, and scale.
Should I learn Turkish? What is best for the University?
Some people ask me why I do not learn Turkish. It is a good question. For sure, it will be good for me. I would be able to speak about football with the butcher, discuss politics with my father-in-law, and read my collection of Matematik Dünyası magazine. But, what is best for our University?
Homework 4
Plot vectors, choose colors, symbols, and size.
My academic ancestors
A database of all mathematicians and their advisors shows my academic ancestors since Persia in 1200. Some famous names among my ancestors.
Homework 3
Practice for midterm exam. Lists and data frames.
Homework 3
Preparation for the midterm exam.
Homework 2
Practice for midterm exam. Vectors, indices, and general ideas about using R.
Introduction to Computer Science and Programming
This course is an Introduction to Scientific Computing for students of all sciences. We use Linux to learn the basic tools that allow us to handle structured data and extract valuable scientific information from it.
Homework 1
Create a RMarkdown document with the same content and the same structure of a published paper.
Homework 2
We will explore some methods to find which parts of a text are similar to a pattern. For instance, the text can be a genome, and the pattern can be a gene or a motif, but the same ideas apply to any text and any fixed pattern.
Homework 1
Write a function to find the location of a word in a large text.
Systems Biology
This course is an introduction to the theoretical tools that are used to understand the emerging behavior of complex biological networks. Systems Biology is a systemic approach to understand the biological phenomena that occurs inside a cell at the molecular level.
Bioinformatics
The main subject is “metagenomics”. We will learn how to handle the output of DNA sequencing machines, how to assemble the chromosome, how to find genes and how to determine the probable function of the proteins they encode. If time allows, we will also study phylogenetic trees and microarray analysis.
Computing in Molecular Biology 1
This course is an introduction to Data Science for students of Molecular Biology. We use the R language to learn the basic tools to handle structured data and extract valuable scientific information from it.
Fundamental Mathematics for Life Sciences
Do you want to extract more value from your data? Do you know how to interpret your results? Do you want to choose the best program to analyze your data? Come to Şirince in September to learn how.
About Makeup exam
Summary of the content, and what to expect in the makeup exam.
Exercises for Makeup
More practice for the makeup exam.
Comments about the Final Exam
Why some people got all answers correctly, while others got nothing? I think it is directly correlated to delivering homework. The people who did homework got prepared for this kind of questions. Of course, the exam has different questions, but the logic and philosophy is the same as in the homework. Here I explain how.
Extra Homework 1
More practice for the exam
Homework 11
Practice for the exam
Homework 10
Shall you take the umbrella today?
Homework 9
Estimating the frequency of epilepsy and double birthdays.
Homework 8
Practice of plots, chaos, and randomness
The Biologist Toolbox: Simulating Systems on the computer
Once we have a description of a system, and a nice drawing to represent it, we can answer some interesting questions. The first question is usually “what will happen?” In other words, we usually want to know what is the behavior of the system.
Homework 7
Practice on algorithm design
The Biologist Toolbox: Drawing Systems
Can we represent a complex system in a simple and easy-to-understand way that is still realistic enough to be useful? The graphical representation that we discuss here, based on Petri nets, can be used to summarize a dynamical system and can easily be translated into a simulation.
Comment on Homework 5
Did you finish Homework 5? This article shows how someone may draw Trees and Branches using Turtle Graphics and recursive functions in R.
Homework 6
This town is full of rats
Homework 5
Algorithm design for half values. Drawing recursive trees.
Homework 4
Count rabbits, reverse strands, and find the origin.
Homework 3
We want to draw one or more stick-people. Prepare a function for that.
Homework 2
Write functions to draw a house, a person, a pentagon, and a polygon.
Replacing Jekyll by Makefile
I’m not very happy with the speed of Jekyll, and with the lack of interaction with the parts of the blog made in Rmarkdown. I also do not like that Jekyll is written in Ruby, one of the languages I do not want to learn.
Homework 1
This week we have two questions. You only need to answer one. If you answer both, it counts as two homework. if you delivered the summer homework you got also one homework.
Methodology of Scientific Research
What is the value of Science? In this course we will discuss why do we need Science, how Science improves people’s lives and how to do it better.
Computing in Molecular Biology 2
This course is an introduction to Computational Thinking. We will use the tools we learned in the previous course and apply them to model and simulate scientific experiments as a way to understand them.
Free Fall Experiment
Learning Machine Learning, session 2
Keywords Git Github Kmeans clustering Gene expression Datasets
Learning Machine Learning, session 1
Keywords Learning Classification Supervised Unsupervised Training Datasets
Hands-On Machine Learning with Scikit-Learn and TensorFlow
Table of Contents of the book we use on the Learning Machine Learning Workshop
Learning Machine Learning
We have a lot of data. How can we understand it? How can we extract meaningful insight from it? In many places around the globe, researchers in academia and industry are using Machine Learning to answer these questions. Artificial Intelligence tools provide big advantages for the scientist that use them. This workshop (also known as "The Machine Atelier") aims to update us into the current state-of-the-art computational and mathematical tools that are useful in Molecular Biology, Physics, and other sciences.
Homework 2 – DNA assemblers
There are several free DNA assemblers available on the web. We need to use some of them. Your homework is to find them, and identify its primary characteristics.
Homework 1 – Next Generation Sequences
Since only one person gave an oral presentation on the scheduled day, everybody else will have to delivered the homework as a written document. Everybody has to chose a different DNA sequencing technology, and explain it.
What people say about this course
Shall you attend to “Systems Biology”? You could ask your friends that have already taken the course before. We asked them already, and here you can see what they say and decide if you want to attend and learn hard and interesting things.
What people say about "Computing in Molecular Biology"
Shall you attend to “Computing in Molecular Biology”? You could ask your friends that have already taken the course before. We asked them already, and here you can see what they say and decide if you want to attend and learn hard and interesting things.
Systems Biology
This course is an introduction to the theoretical tools that are used to understand the emerging behavior of complex biological networks. Systems Biology is a systemic approach to understand the biological phenomena that occurs inside a cell at the molecular level.
Introduction to Computer Science and Programming
This course is an Introduction to Scientific Computing for students of all sciences. We use Linux to learn the basic tools that allow us to handle structured data and extract valuable scientific information from it.
Bioinformatics
This is the English language version of the Bioinformatics course. The main subject is “metagenomics”. We will learn how to handle the output of DNA sequencing machines, how to assemble the chromosome, how to find genes and how to determine the probable function of the proteins they encode. If time allows, we will also study phylogenetic trees and microarray analysis.
Computing in Molecular Biology 1
Keep your mind sharp on August
Why do rich kids learn more than poor kids? According to some research, the “achievement gap” between kids of high-income and low-income families is not that rich kids learn more, but that they forget less in the summer holiday. Following this idea, I propose a couple of challenges to keep your mind active during the holidays, and maybe win a nice book.
Answers to Final Exam
The “official” answers to the exam are published here. Some questions can have other correct answers, so take this just as a reference.
Exercises for Final Exam
Work on this list every day without exception, at least 25 minutes without interruption. Use an alarm clock to know when to stop. Do not stop until the alarm rings. Always stop when the alarm rings and do something else for at least 5 minutes.
My Professor got an International Prize
One of my professors got an international award. He had already won the most prestigious national recognitions in Science. Now he became global. This gives me the opportunity to start a series of posts about my world-class professors and their international achievements.
Homework 4
Epilepsy affects 1% of world population. What does that mean for us in this course? Can we have everybody with epilepsy?
For Scientific Presentations Less is More
The Abstract Expressionist artist Ad Reinhardt said “The more stuff in it, the busier the work of art, the worse it is. More is less. Less is more.” Here we apply this idea to two concrete examples.
Homework 3
Today on Class 13 we saw an interesting system that has very different behavior depending on the rate parameter. This system was discovered in modeling of insect population, in particular when there is super-population (see Utilda 1957). It is called “Quadratic Map”.
Comments on Midterm Exam
The midterm exam has three mandatory questions and one optional. All questions point to evaluate Computational Thinking skills: decomposition, pattern recognition, abstraction and algorithm design
The Biologist Toolbox: Simulating Systems on the computer
Once we have a description of a system, and a nice drawing to represent it, we can answer some interesting questions. One of the most common questions is what is the behavior of the system? In other words, we usually want to know what will happen?.
The Biologist Toolbox: Drawing Systems
Can we represent a complex system in a simple and easy to understand way that is still realistic enough to be useful? The graphical representation that we discuss here, based Petri nets, can be used to summarize a dynamical system and can easily translated into a simulation.
Recovering from `fail2ban`
Today Güney got banned from the dry-cloud server, so I had to learn how to ‘unban’ him.
Get to know your cables
Picture this. You have been invited to present your work in a prestigious university, in front of nice people with whom you would like to collaborate, or maybe work in the same department. You prepared your slides, some videos, and configured everything in your computer. You get to the podium, dressed for success, and then you realize that you cannot connect your computer to the projector of your host. You are forced to copy your presentation to someone’s else computer, which does not have the fonts and the codecs that make your presentation memorable. The video cannot be seen, the tables luck ugly and your professional reputation is stained.
Class 6: Quiz 2
Bioinformatics + Biotech in high impact strategic industries: My talk at Yeditepe University
Biotechnology has changed a lot in the last 10 years, and it will probably keep changing. The same applies for all science and technology. Experiments that used to be expensive and slow, are today cheap and fast. Producing and analyzing huge volumes of data is easy and inexpensive today. Everybody can build new instruments, or cheaper versions of the standard instruments at home, and even do synthetic biology in any lab. How will you succeed in this brave new world?
Homework 2
The function draw_star() that we build in the class has 3 inputs: N, R and angle, and draws always around the center of the window. Please modify it to work with two more inputs, named x and y, that indicate the center of the star. Modify also the functions draw_polygon() and draw_circle() to also handle x and y to choose the position. Use these functions (and others) to draw a stick man like the one you did in Homework 1. (Optional) We propose that initial_angle must be 90+angle/2 and size must be 2*R*sin(angle*pi/360). Why these values?
Methodology of Scientific Research
Do we need to have a Faculty of Sciences? Or is it better to have a shopping mall at Vezneciler Campus? What is the value of Science? In this course we will discuss why do we need Science, how Science improves people’s lives and how to do it better.
Class2: Quiz 1
Turtle graphics Following an ancient tradition, sprites in Scratch can draw lines when they move. You can see the options under the Pen section. The essential ones are pen down, pen up and clear. Today we are going to use them to make some nice figures.
Homework 1
We have a lot to learn and too little time so we better start working soon.
Molecular Slideology
The official name of this course is “Seminar”, from the latin word Seminarium, a college that prepares students to be priests, ministers, or rabbis; which itself derives from the latin word for seed. Seminarists are trained to spread the word like a seed. Today our goal is to learn how to prepare and deliver good scientific presentations, speak in public and spread the seed of knowledge. Presentations are usually supported by visual elements, typically projected slides. We have a lot of theory and we need a lot of practice.
Computing in Molecular Biology 2
This course is an introduction to Quantitative Thinking. We will use the tools we learned in the previous course and apply them to model real data and to simulate scientific experiments as a way to understand them.
Numbering the pages of a PDF
I often have PDF files without page numbers. For example, when I print the exam questions on Google Chrome they do not have page numbers. I was resigned myself to this situation, until my wife asked me to put page numbers into some of her PDF documents. Here is how I solved it.
Answers of Exam
I’m publishing my answers to the exam, in case they may help you with the makeup. There are many equivalent answers, that achieve the same result with different code. Here I’m showing one possible answer, usually shorter than others.
Keywords for the Miterm exam
This course is an introduction to genomics, with emphasis on metagenomics. To prepare for the final exam, here you can find the keywords and main ideas we have discussed on classes.
Systems Biology
This course is an introduction to the theoretical tools that are used to understand the emerging behavior of complex biological networks. Systems Biology is a systemic approach to understand the biological phenomena that occurs inside a cell at the molecular level.
Vectors
If matrices represent how the system changes, vectors represent the state of the systems. They also have a geometric interpretation that will allow us to solve minimization problems easily.
Some comments about the Exercise for Midterms
As you remember, I gave you an exercise to prepare you for the midterm exam of Computing in Molecular Biology 1. A few (very few) of you have sent me their answers. Some people asked questions about the parts 3 and 8, which I think are interesting to all the students. Here are my comments.
Keywords for the Miterm exam
This course is an introduction to genomics, with emphasis on metagenomics. To prepare for the midterm exam, here you can find the keywords and main ideas we have discussed on classes.
Intro to Computer Science: Keywords for Midterm Exam
This course is an introduction to scientific computing using the Unix command line. The midterm exam will measure the learning of the first part of the course, mostly definitions. In this post you can see all the concepts that have been defined in the course. They are written as questions, so the students can evaluate their own learning and have a guide on how to improve.
Matrices
Matrix multiplication is not what we imagine, and there is a reason for that. Learn why we multiply matrices in this particular way.
Computing in Molecular Biology 1
This course is an introduction to Data Science for students of Molecular Biology. We use the R language to learn the basic tools to handle structured data and extract valuable scientific information from it.
Introduction to Computer Science and Programming
This course is an Introduction to Scientific Computing for students of all sciences. We use Linux to learn the basic tools that allow us to handle structured data and extract valuable scientific information from it.
Bioinformatics
This is the first version in English language of the Bioinformatics course. The main subject is “metagenomics”. We will learn how to handle the output of DNA sequencing machines, how to assemble the chromosome, how to find genes and how to determine the probable function of the proteins they encode. If time allows, we will also study phylogenetic trees and microarray analysis.
You can see the Exam Answers with Comments
The exam is finished. You can see the questions and its solutions at the course website. I wrote comments to each question that can help you understand what is expected and what are the most common errors that people made.
Homework after class 19
This time we are going to use our tools to understand how cells use different codons for the same amino-acid.
Homework after Class 16
The homework of this week aims to replicate the tables and graphics of the website Comparative Genometrics, which has precomputed statistics for the DNA sequences of several thousands of Bacteria.
Exercises after Class 8
The next week we will have a graded quiz. It will be like an exam and it will allow you to practice for the real exam.
Homework after Class 6
The Quiz was delayed and this homework was cancelled. This homework is replaced by the Exercieses after Class 8.
Methodology of Scientific Research
How Science Works This course was given between February and May 2017.
Homework after Class 4
For this homework you have to prepare a Rmarkdown document. The homework has a mandatory part and two optional ones.
Computing in Molecular Biology 2
This course is an introduction to Quantitative Thinking. We will use the tools we learned in the previous course and apply them to model real data and to simulate scientific experiments as a way to understand them.
A nice way to show email address and avoid spam
How can you let the readers know your email address, but avoid it being collected by spammers?
What "Computing in Molecular Biology" is about
These are the subjects that every student of CMB needs to know after the course. Some of these contents are evaluated on the makeup, some were already evaluated.
Computing in Molecular Biology 1
This course is an introduction to Data Science. The goal is to learn the basic tools that allow any scientist to handle structured data and extract valuable scientific information from it.
How exams are graded
For the “Computing in Molecular Biology” courses we evaluate what students have learned using exams in digital forms. To do this in a fair and transparent way I use an automatic process. Here I describe it.
Automatic bureaucracy
Every time there is a conference I have to fill some paperwork. To make my life easier (it is already short), I’ve made some simplifications that work for me.
Gebze Technical University
Today I had the opportuity to present my work on building putative transcriptional regulatory networs at Gebze Technical University. Dr. Pınar Pir invited me to give a seminar on the course coordinated by Dr. Saliha Durmuş Tekir. It was well received, in particular when I spoke about “why biologist should learn math”.
My Talks at "Computational Ecology and Evolution Workshop"
These are the slides I used at Şirince on the “1st Computational Ecology and Evolution Workshop”
Computing in Molecular Biology 2
This course is an introduction to Quantitative Thinking. We will use the tools we learned in the previous course and apply them to model real data and to simulate scientific experiments as a way to understand them.
DataIstanbul
My friend Greg, despite being “gringo”, speaks good Turkish and Spanish. Better than me, for sure. Since he also speaks math and computers we usually talk a lot. He convinced me to attend to a series of meetings held at Istanbul Technical University, Maçka Campus, about data science. They are organized by a nice group of students and data scientist that call themselves Dataistanbul.
Homework for class 8
The library seqinr is needed in all the following exercises.
Homework for class 7
Research questions The class of next week will be based on these subjects
Homework for Class 6
For March 15, 2016, the homework questions are this:
Homework for Class 5
Determine the GC content of E.coli Is this GC content uniform through all genome? Calculate the ratio
Homework for Class 4
In next class we will start analyzing genomic sequences. Prepare slides to explain
Exercises for Computing in Molecular Biology
These exercises are not graded but help you to understand the subject and learn effectively. They can be solved individually or in group. Remember that learning is a team activity.
Homework for Class 3
Read the short story “Funes the Memorious” (by Argentine writer Jorge Luis Borges). You can find it on the web.
Computing for Molecular Biology 1
These are the slides used in the Winter 2015 semester
Summary of Network Inference, Analysis, and Modeling in Systems Biology
Original paper by Réka Albert, The Plant Cell 19: 3327-3338 (2007)
Seminar at METU
Today I gave a small talk at the Biology Department of the Middle East Technical University. Professor Mehmet Somel kindly invited me and introduced me to his colleagues and students.
Workshop: Introduction to Data Science
In the spring of 2015 we meet weekly to understand some tools required for doing science in data intensive disciplines such as Molecular Biology and Genetics.
Installing extra R packages
R packages are sets of functions that extend the basic capabilities of R.
Teaching and Using Informatics Tools for Molecular Biology
In February of 2015 I prepared a document about my vision of my job at Istanbul University. I made a nice slidedoc that you can see on line or download as pdf. This is the expanded version.
Computing in Molecular Biology and Genetics II
This is the description of the second undergrad course I’m going to teach next year.
Computing in Molecular Biology and Genetics I
On April 27 my boss asked me to describe the classes I’m going to teach starting the Fall 2015 semester. The first one, named “Computing in Molecular Biology and Genetics I”, replaces the former course “Computation III”. The old course used to teach databases and SQL on the Microsoft Access platform.
Blogging with Acrylamid
This week I started blogging using Acrylamid. I like the idea of static pages, so I can use the “pages” service provided by github.io. Also, since I do not want to learn Ruby right now, I like that acrylamid is written un Python.
Proposition of new grad level courses
I was asked today to propose new grade level courses for the Department of Molecular Biology and Genetics. This is my proposal.
Seminar at Department of Mathematics
I spent a couple of months on the office of the Director of the Mathematics Department at Istanbul University. We were moving from the old Biology building to new offices, which were not yet finished, so Terje and I had to stay somewhere else for a while.
Talk at IU Genetics Club's Winter School
Every year the student’s club of the Department of Molecular Biology and Genetics organize a Winter School for undergrads. It is a three days event, usually involving Turk and foreigner professors. Each one speaks for 45 minutes in front of near 600 young students.
Teaching and Using Informatics Tools for Molecular Biology and Genetics
The Challenges of Modern Molecular Biology and Genetics The Department of Molecular Biology and Genetics at Istanbul University was created 13 years ago. In the following years it established itself as a well respected department. It attracts every year between 40 and 60 of the best students in the country. They can later follow Masters and Doctorate post-degrees. It has published 376 papers, mainly on plant genomics and fission yeast as a model for human metabolism. Our department is young but is up-to-date with modern molecular biology and genetics theory and practice.
Interactomics: My last talk at Chile
I started working at the Center of Mathematical Modeling on 2001. On January 2003 I became the Chief Research Engineer of the Laboratory of Bioinformatics and Mathematics of Genome (today called Mathomics). With the rest of the team we did many pretty amazing things, which you can find elsewhere.