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CMB2: Answers to Final Exam

May 10, 2018 - 408 words

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

CMB2: Exercises for Final Exam

May 10, 2018 - 1492 words

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: My Professor got an International Prize

May 5, 2018 - 668 words

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: Homework 4

Apr 20, 2018 - 327 words

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

Slideology: For Scientific Presentations Less is More

Apr 14, 2018 - 1204 words

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: Homework 3

Apr 11, 2018 - 374 words

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: Comments on Midterm Exam

Apr 5, 2018 - 1156 words

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

Apr 1, 2018 - 1167 words

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

Mar 30, 2018 - 739 words

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: Recovering from `fail2ban`

Mar 26, 2018 - 214 words

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

Slideology: Get to know your cables

Mar 2, 2018 - 316 words

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.

Talks: Bioinformatics + Biotech in high impact strategic industries: My talk at Yeditepe University

Feb 26, 2018 - 1628 words

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: Homework 2

Feb 23, 2018 - 99 words

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: Methodology of Scientific Research

Feb 22, 2018 - 309 words

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.

Slideology: Homework 1

Feb 14, 2018 - 174 words

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

Course Homepage: Molecular Slideology

Feb 14, 2018 - 364 words

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: Computing in Molecular Biology 2

Feb 13, 2018 - 876 words

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

Jan 28, 2018 - 655 words

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

Jan 23, 2018 - 46 words

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: Keywords for the Miterm exam

Dec 28, 2017 - 435 words

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: Systems Biology

Dec 26, 2017 - 338 words

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: Vectors

Nov 7, 2017 - 1104 words

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: Some comments about the Exercise for Midterms

Nov 6, 2017 - 469 words

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: Keywords for the Miterm exam

Nov 2, 2017 - 291 words

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

Oct 30, 2017 - 819 words

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: Matrices

Oct 18, 2017 - 1079 words

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

Course Homepage: Computing in Molecular Biology 1

Sep 26, 2017 - 248 words

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: Introduction to Computer Science and Programming

Sep 20, 2017 - 321 words

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: Bioinformatics

Sep 18, 2017 - 738 words

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: You can see the Exam Answers with Comments

Jun 12, 2017 - 42 words

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: Homework after class 19

May 5, 2017 - 382 words

This time we are going to use our tools to understand how cells use different codons for the same amino-acid.

CMB2: Homework after Class 16

Apr 16, 2017 - 163 words

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: Exercises after Class 8

Mar 10, 2017 - 265 words

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: Homework after Class 6

Feb 28, 2017 - 220 words

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

Course Homepage: Methodology of Scientific Research

Feb 23, 2017 - 216 words

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

CMB2: Homework after Class 4

Feb 22, 2017 - 265 words

For this homework you have to prepare a Rmarkdown document. The homework has a mandatory part and two optional ones.

Course Homepage: Computing in Molecular Biology 2

Feb 13, 2017 - 520 words

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

Feb 11, 2017 - 394 words

How can you let the readers know your email address, but avoid it being collected by spammers?

CMB2: What "Computing in Molecular Biology" is about

Jan 22, 2017 - 987 words

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: Computing in Molecular Biology 1

Dec 15, 2016 - 366 words

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

Dec 14, 2016 - 1072 words

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

Dec 14, 2016 - 789 words

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: Gebze Technical University

Oct 20, 2016 - 157 words

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”.

CMB2: Computing in Molecular Biology 2

Jun 17, 2016 - 488 words

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: DataIstanbul

Apr 20, 2016 - 149 words

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: Homework for class 8

Mar 24, 2016 - 609 words

The library seqinr is needed in all the following exercises.

CMB2: Homework for class 7

Mar 15, 2016 - 201 words

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

CMB2: Homework for Class 6

Mar 8, 2016 - 205 words

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

CMB2: Homework for Class 5

Mar 1, 2016 - 31 words

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

CMB2: Homework for Class 4

Feb 23, 2016 - 30 words

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

CMB2: Exercises for Computing in Molecular Biology

Feb 18, 2016 - 419 words

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: Homework for Class 3

Feb 16, 2016 - 182 words

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

Course Homepage: Computing for Molecular Biology 1

Dec 29, 2015 - 120 words

These are the slides used in the Winter 2015 semester

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

Nov 9, 2015 - 1712 words

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

Talks: Seminar at METU

Nov 4, 2015 - 64 words

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

Jul 9, 2015 - 325 words

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

May 14, 2015 - 415 words

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

Teaching and Using Informatics Tools for Molecular Biology

May 4, 2015 - 3207 words

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

Apr 27, 2015 - 684 words

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

Computing in Molecular Biology and Genetics I

Apr 27, 2015 - 802 words

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

Apr 25, 2015 - 114 words

This week I started blogging using Acrylamid. I like the idea of static pages, so I can use the “pages” service provided by 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

Apr 21, 2015 - 1006 words

I was asked today to propose new grade level courses for the Department of Molecular Biology and Genetics. This is my proposal.

Talks: Seminar at Department of Mathematics

Apr 15, 2015 - 138 words

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: Talk at IU Genetics Club's Winter School

Mar 6, 2015 - 147 words

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

Mar 1, 2015 - 3354 words

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: Interactomics: My last talk at Chile

Nov 12, 2014 - 86 words

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.

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