Blog of Andrés Aravena

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Course Homepage | Feb 18, 2022

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.

Dec 12, 2021

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.

Dec 8, 2021

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.

Bioinfo | Nov 28, 2021

All homework for the bioinformatics course

In case you have forgotten, here is a list of all that you must deliver.

Bioinfo | Oct 18, 2021

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.

Course Homepage | Sep 23, 2021

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.

Course Homepage | Sep 23, 2021

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.

CMB2 | Jun 7, 2021 (Deadline: Fri Jun 11, 9:00)

Homework 9

We cannot predict the future, but we can make educated guesses. Practice educating your guesses.

CMB2 | May 31, 2021 (Deadline: Fri Jun 4, 9:00)

Homework 8

What will be your score in the exam? Use simulation to see what will probably happen.

CMB2 | May 25, 2021 (Deadline: Mon May 31, 9:00)

Homework 7

Practice of Montecarlo method. Simulate “complex” random systems by decomposing them into simpler ones.

CMB2 | May 5, 2021

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.

CMB2 | May 3, 2021

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.

CMB2 | Apr 9, 2021 (Deadline: Fri Apr 16, 9:00)

Homework 6

Simulate a predator-pray system, using Lotka-Volterra model.

Course Homepage | Apr 5, 2021

Computing in Molecular Biology 2

Introduction to Computational and Quantitative Thinking. Systems to understand the universe, and simulations to predict their consequences.

CMB2 | Apr 2, 2021 (Deadline: Fri Apr 9, 9:00)

Homework 5

Count rabbits with recursive functions and with a loop.

CMB2 | Mar 26, 2021 (Deadline: Fri Apr 2, 8:59)

Homework 4

Practice writing functions, for loops and conditional blocks.

CMB2 | Mar 22, 2021 (Deadline: Fri Mar 26, 8:59)

Homework 3

Practice writing functions and applying them to several elements of a list.

Math | Mar 14, 2021

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.

Math | Mar 13, 2021

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.

Math | Mar 12, 2021

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.

CMB2 | Mar 12, 2021 (Deadline: Fri Mar 19, 8:59)

Homework 2

Teach the computer how to write the flag of Turkey.

CMB2 | Mar 12, 2021 (Deadline: Wed Mar 31, 23:59)

Homework 1

Write to learn.

Course Homepage | Mar 8, 2021

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.

CMB1 | Feb 7, 2021

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.

Bioinfo | Jan 12, 2021 (Deadline: Fri Jan 22, 9:00)

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.

CMB1 | Jan 5, 2021 (Deadline: Mon Jan 11, 11:00)

Homework 5

Practice for final exam. Plots and linear models.

CMB1 | Nov 25, 2020 (Deadline: Mon Nov 30, 11:00)

Homework 4

Practice for midterm exam. Tidying up real-life data.

Course Homepage | Nov 18, 2020

Computing in Molecular Biology 1

How to really use the computer, beyond Microsoft Word®, PowerPoint®, and Facebook®. An introduction to Data Science.

CMB1 | Nov 17, 2020 (Deadline: Mon Nov 23, 11:00)

Homework 3

Practice for midterm exam. Vectors and indices, again.

CMB1 | Nov 7, 2020 (Deadline: Mon Nov 16, 11:00)

Homework 2

Practice for midterm exam. Vectors, indices, and general ideas about using R.

Course Homepage | Nov 6, 2020

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.

CMB2 | Aug 6, 2020

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.

CMB2 | Aug 4, 2020

Comments on Midterm Exam, part 2

This is the second part of three posts explaining some ways to answer the midterm exam.

CMB2 | Aug 4, 2020

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.

CMB2 | Jul 21, 2020

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.

CMB2 | Jul 21, 2020

Comments on Final Exam, part 1

CMB2 | Jun 26, 2020

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.

CMB2 | Jun 26, 2020

Fixing Errors in the Exam

There are two error in the Exam questions. Read here to avoid confusion.

CMB2 | Jun 26, 2020

Comments on Question 2.4 – Final Exam

A new explanation of question 2.4, and some examples.

CMB2 | Jun 12, 2020

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.

CMB2 | Jun 5, 2020

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.

May 22, 2020

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.

May 13, 2020

Wizardry

Freefall by Mark Stanley, October 18, 1999

Methodology of Scientific Research | May 9, 2020

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?

May 4, 2020

La Biblioteca de Babel de Borges

How many books? How many planets?

May 4, 2020

Solving Triangle Peg Puzzle with Unix command line tools

Matt Parker's 5th Puzzle

Methodology of Scientific Research | Apr 24, 2020

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.

CMB2 | Apr 21, 2020 (Deadline: Tue Apr 28, 8:30)

Homework 9

Explain in English what are the parts of each of these systems, and what do you think will be the systems' behavior.

CMB2 | Apr 14, 2020 (Deadline: Tue Apr 21, 8:30)

Homework 8

Explain in English what will the system do.

Apr 13, 2020

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.

Methodology of Scientific Research | Apr 9, 2020

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.

Methodology of Scientific Research | Apr 8, 2020

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?

Methodology of Scientific Research | Apr 1, 2020

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.

Mar 31, 2020

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.

CMB2 | Mar 30, 2020 (Deadline: Mon Apr 6, 17:30)

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.

Methodology of Scientific Research | Mar 26, 2020

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.

Methodology of Scientific Research | Mar 25, 2020

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.

CMB2 | Mar 23, 2020 (Deadline: Fri Mar 27, 17:30)

Homework 6

Exercise your brain for the midterms. Using the computer to handle DNA data safely at home.

Mar 20, 2020

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.

CMB2 | Mar 18, 2020

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.

Mar 16, 2020

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.

CMB2 | Mar 11, 2020 (Deadline: Thu Mar 19, 12:30)

Homework 5

Practice of functions, for DNA analysis and for fun. Getting ready for the midterms.

CMB2 | Mar 4, 2020 (Deadline: Tue Mar 10, 8:30)

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.

CMB2 | Feb 27, 2020 (Deadline: Tue Mar 3, 8:30)

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.

CMB2 | Feb 25, 2020

Welcome Survey delivery

Delivered

CMB2 | Feb 25, 2020

Homework 2 delivery

Delivered

Methodology of Scientific Research | Feb 23, 2020

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.

CMB2 | Feb 19, 2020 (Deadline: Wed Feb 26, 8:30)

Homework 2

Peer-review of first exercise. Learn to recognize good and bad decompositions. Learn to give feedback. Train to be a referee.

CMB2 | Feb 13, 2020 (Deadline: Wed Feb 19, 8:30)

Homework 1

Take a complex drawing and decompose it in many smaller parts

Course Homepage | Feb 9, 2020

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.

Course Homepage | Feb 9, 2020

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.

Bioinfo | Dec 6, 2019

Homework 4 (Practical)

Preparation for final exam.

CMB1 | Dec 6, 2019 (Deadline: Tue Dec 31, 8:00)

Homework 7

Exam Rehearsal.

CMB1 | Dec 6, 2019 (Deadline: Tue Dec 17, 8:00)

Homework 6

Subsets and linear models.

CMB1 | Nov 28, 2019 (Deadline: Tue Dec 10, 9:00)

Homework 5

Scatter plots, choose colors, size, titles, and scale.

Nov 24, 2019

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?

CMB1 | Nov 21, 2019 (Deadline: Tue Dec 3, 9:00)

Homework 4

Plot vectors, choose colors, symbols, and size.

Nov 3, 2019

A database of all mathematicians and their advisors shows my academic ancestors since Persia in 1200. Some famous names among my ancestors.

CMB1 | Oct 23, 2019 (Deadline: Mon Nov 4, 9:00)

Homework 3

Practice for midterm exam. Lists and data frames.

Bioinfo | Oct 18, 2019

Homework 3

Preparation for the midterm exam.

CMB1 | Oct 9, 2019 (Deadline: Tue Oct 15, 9:00)

Homework 2

Practice for midterm exam. Vectors, indices, and general ideas about using R.

Course Homepage | Sep 26, 2019

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.

CMB1 | Sep 25, 2019 (Deadline: Tue Oct 8, 9:00)

Homework 1

Create a RMarkdown document with the same content and the same structure of a published paper.

Bioinfo | Sep 22, 2019 (Deadline: Fri Oct 4, 14:00)

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.

Bioinfo | Sep 19, 2019 (Deadline: Tue Sep 24, 13:00)

Homework 1

Write a function to find the location of a word in a large text.

Course Homepage | Sep 18, 2019

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.

Course Homepage | Sep 17, 2019

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.

Course Homepage | Sep 16, 2019

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.

Course Homepage | Jul 11, 2019

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.

CMB2 | Jun 18, 2019

Summary of the content, and what to expect in the makeup exam.

CMB2 | Jun 8, 2019 (Deadline: Makeup exam day)

Exercises for Makeup

More practice for the makeup exam.

CMB2 | Jun 1, 2019

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.

CMB2 | May 15, 2019 (Deadline: Exam day)

Extra Homework 1

More practice for the exam

CMB2 | May 12, 2019 (Deadline: Fri May 17, 9:00)

Homework 11

Practice for the exam

CMB2 | May 5, 2019 (Deadline: Fri May 10, 9:00)

Homework 10

Shall you take the umbrella today?

CMB2 | Apr 26, 2019 (Deadline: Fri May 3, 9:00)

Homework 9

Estimating the frequency of epilepsy and double birthdays.

CMB2 | Apr 21, 2019 (Deadline: Fri Apr 26, 9:00)

Homework 8

Practice of plots, chaos, and randomness

CMB2 | Apr 4, 2019

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.

CMB2 | Mar 29, 2019 (Deadline: Wed Apr 10, 11:00)

Homework 7

Practice on algorithm design

CMB2 | Mar 26, 2019

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.

CMB2 | Mar 26, 2019

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.

CMB2 | Mar 24, 2019 (Deadline: Fri Mar 29, 9:00)

Homework 6

This town is full of rats

CMB2 | Mar 16, 2019 (Deadline: Fri Mar 22, 9:00)

Homework 5

Algorithm design for half values. Drawing recursive trees.

CMB2 | Mar 8, 2019 (Deadline: Fri Mar 15, 9:00)

Homework 4

Count rabbits, reverse strands, and find the origin.

CMB2 | Mar 1, 2019 (Deadline: Fri Mar 8, 9:00)

Homework 3

We want to draw one or more stick-people. Prepare a function for that.

CMB2 | Feb 23, 2019 (Deadline: Fri Mar 1, 9:00)

Homework 2

Write functions to draw a house, a person, a pentagon, and a polygon.

Blog | Feb 17, 2019

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.

CMB2 | Feb 17, 2019 (Updated on Feb 20, 2019) (Deadline: Fri Feb 22, 9:00)

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.

Course Homepage | Feb 9, 2019

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.

Course Homepage | Feb 9, 2019

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.

Dec 10, 2018

Free fall experiment

We can use the computer to extract specific information from pictures and movies. Here we use some command-line tools to analyze a simple experiment. The experiment is simple, but the analysis had many unexpected compications.

Dry-Lab | Oct 15, 2018

Learning Machine Learning, session 2

Keywords Git Github Kmeans clustering Gene expression Datasets

Dry-Lab | Oct 7, 2018

Learning Machine Learning, session 1

Keywords Learning Classification Supervised Unsupervised Training Datasets

Dry-Lab | Oct 6, 2018

Hands-On Machine Learning with Scikit-Learn and TensorFlow

Dry-Lab | Oct 6, 2018

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.

Bioinfo | Oct 5, 2018 (Deadline: Tue Oct 16, 13:00)

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.

Bioinfo | Oct 5, 2018 (Deadline: Fri Oct 12, 13:30)

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.

SysBio | Sep 11, 2018

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.

CMB1 | Sep 11, 2018

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.

Course Homepage | Sep 1, 2018

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.

Course Homepage | Sep 1, 2018

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.

Course Homepage | Sep 1, 2018

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.

Course Homepage | Sep 1, 2018

Aug 23, 2018

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.

CMB2 | May 10, 2018

The “official” answers to the exam are published here. Some questions can have other correct answers, so take this just as a reference.

CMB2 | May 10, 2018 (Deadline: Exam day, of course)

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.

Chile | May 5, 2018

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.

CMB2 | Apr 20, 2018 (Deadline: Wed Apr 25, 9:00)

Homework 4

Epilepsy affects 1% of world population. What does that mean for us in this course? Can we have everybody with epilepsy?

Slideology | Apr 14, 2018

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.

CMB2 | Apr 11, 2018 (Deadline: Wed Apr 18, 9:00)

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”.

CMB2 | Apr 5, 2018

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

Apr 1, 2018

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?.

Mar 30, 2018

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.

Best Practices | Mar 26, 2018

Recovering from fail2ban

Today Güney got banned from the dry-cloud server, so I had to learn how to ‘unban’ him.

Slideology | Mar 2, 2018

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.

CMB2 | Mar 2, 2018 (Deadline: Fri Mar 2, 17:00)

Class 6: Quiz 2

Talks | Feb 26, 2018

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?

CMB2 | Feb 23, 2018 (Deadline: Wed Feb 28, 9:00)

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?

Course Homepage | Feb 22, 2018

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.

CMB2 | Feb 16, 2018 (Deadline: Fri Feb 16, 17:00)

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.

Slideology | Feb 14, 2018 (Deadline: Mon Feb 26, 10:00)

Homework 1

We have a lot to learn and too little time so we better start working soon.

Course Homepage | Feb 14, 2018

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.

Course Homepage | Feb 13, 2018

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.

Jan 28, 2018

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.

Jan 23, 2018

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.

Bioinfo | Dec 28, 2017

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.

Course Homepage | Dec 26, 2017

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.

Toolbox | Nov 7, 2017

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.

CMB1 | Nov 6, 2017

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.

Bioinfo | Nov 2, 2017

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.

Oct 30, 2017

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.

Toolbox | Oct 18, 2017

Matrices

Matrix multiplication is not what we imagine, and there is a reason for that. Learn why we multiply matrices in this particular way.

Course Homepage | Sep 26, 2017

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.

Course Homepage | Sep 20, 2017

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.

Course Homepage | Sep 18, 2017

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.

CMB2 | Jun 12, 2017

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.

CMB2 | May 5, 2017 (Deadline: Mon May 15, 14:00)

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.

CMB2 | Apr 16, 2017 (Deadline: Mon May 1, 14:00)

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.

CMB2 | Mar 10, 2017

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.

CMB2 | Feb 28, 2017 (Deadline: Mon Mar 6, 14:00)

Homework after Class 6

The Quiz was delayed and this homework was cancelled. This homework is replaced by the Exercieses after Class 8.

Course Homepage | Feb 23, 2017

Methodology of Scientific Research

How Science Works This course was given between February and May 2017.

CMB2 | Feb 22, 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.

Course Homepage | Feb 13, 2017

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.

Feb 11, 2017

A nice way to show email address and avoid spam

CMB2 | Jan 22, 2017

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.

Course Homepage | Dec 15, 2016

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.

Dec 14, 2016

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.

Dec 14, 2016

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.

Talks | Oct 20, 2016

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”.

Talks | Oct 1, 2016

My Talks at "Computational Ecology and Evolution Workshop"

These are the slides I used at Şirince on the “1st Computational Ecology and Evolution Workshop”

CMB2 | Jun 17, 2016

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.

Talks | Apr 20, 2016

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.

CMB2 | Mar 24, 2016

Homework for class 8

The library seqinr is needed in all the following exercises.

CMB2 | Mar 15, 2016

Homework for class 7

Research questions The class of next week will be based on these subjects

CMB2 | Mar 8, 2016

Homework for Class 6

For March 15, 2016, the homework questions are this:

CMB2 | Mar 1, 2016

Homework for Class 5

Determine the GC content of E.coli Is this GC content uniform through all genome? Calculate the ratio

CMB2 | Feb 23, 2016

Homework for Class 4

In next class we will start analyzing genomic sequences. Prepare slides to explain

CMB2 | Feb 18, 2016

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.

CMB2 | Feb 16, 2016

Homework for Class 3

Read the short story “Funes the Memorious” (by Argentine writer Jorge Luis Borges). You can find it on the web.

Course Homepage | Dec 29, 2015

Computing for Molecular Biology 1

These are the slides used in the Winter 2015 semester

SysBio | Nov 9, 2015

Summary of Network Inference, Analysis, and Modeling in Systems Biology

Original paper by Réka Albert, The Plant Cell 19: 3327-3338 (2007)

Talks | Nov 4, 2015

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.

Jul 9, 2015

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.

May 14, 2015

Installing extra R packages

R packages are sets of functions that extend the basic capabilities of R.

May 4, 2015

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.

Apr 27, 2015

Computing in Molecular Biology and Genetics II

This is the description of the second undergrad course I’m going to teach next year.

Apr 27, 2015

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.

Apr 25, 2015

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.

Apr 21, 2015

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.

Talks | Apr 15, 2015

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.

Talks | Mar 6, 2015

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.

Mar 1, 2015

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.

Talks | Nov 12, 2014

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.