Biomedical Informatics: Lecture 1

M. Ceccanti and A. Paoluzzi

Tue, Mar 4, 2014

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 1 / 25

Outline: Syllabus, GitHub

1 Syllabus

2 Student projects

3 Grading

4 GitHub

5 Assignments

6 Introduction to bioinformatics

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 2 / 25

Syllabus

Syllabus

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 3 / 25

Syllabus

Biomedical Informatics 2014

General information

Course notes and student home

Programming tools

Pyton

pyplasm (PLaSM for Python)

Javascript

plasm.js (PLaSM for JavaScript)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 4 / 25

Syllabus

Biomedical Informatics 2014

General information

Course notes and student home

Programming tools

Pyton

pyplasm (PLaSM for Python)

Javascript

plasm.js (PLaSM for JavaScript)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 4 / 25

Syllabus

Biomedical Informatics 2014

General information

Course notes and student home

Programming tools

Pyton

pyplasm (PLaSM for Python)

Javascript

plasm.js (PLaSM for JavaScript)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 4 / 25

Syllabus

Biomedical Informatics 2014

General information

Course notes and student home

Programming tools

Pyton

pyplasm (PLaSM for Python)

Javascript

plasm.js (PLaSM for JavaScript)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 4 / 25

Syllabus

Biomedical Informatics 2014

General information

Course notes and student home

Programming tools

Pyton

pyplasm (PLaSM for Python)

Javascript

plasm.js (PLaSM for JavaScript)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 4 / 25

Syllabus

Biomedical Informatics 2014

General information

Course notes and student home

Programming tools

Pyton

pyplasm (PLaSM for Python)

Javascript

plasm.js (PLaSM for JavaScript)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 4 / 25

Syllabus

Biomedical Informatics 2014

General information

Course notes and student home

Programming tools

Pyton

pyplasm (PLaSM for Python)

Javascript

plasm.js (PLaSM for JavaScript)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 4 / 25

Student projects

Student projects

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 5 / 25

Student projects

Student projects

Scheduling

1 Project design: due Fri, May 2, 2014

2 Working prototype: due Fri, June 6, 20143 Project deadline: Before final exam

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 6 / 25

Student projects

Student projects

Scheduling

1 Project design: due Fri, May 2, 20142 Working prototype: due Fri, June 6, 2014

3 Project deadline: Before final exam

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 6 / 25

Student projects

Student projects

Scheduling

1 Project design: due Fri, May 2, 20142 Working prototype: due Fri, June 6, 20143 Project deadline: Before final exam

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 6 / 25

Grading

Grading

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 7 / 25

Grading

Exam requirements

1 Programming project (informatics: prof. Paoluzzi) (≤ 15)

2 Term Paper (biomedical: prof. Ceccanti) (≤ 10)3 Project design and prototype presentations (≤ 5)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 8 / 25

Grading

Exam requirements

1 Programming project (informatics: prof. Paoluzzi) (≤ 15)2 Term Paper (biomedical: prof. Ceccanti) (≤ 10)

3 Project design and prototype presentations (≤ 5)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 8 / 25

Grading

Exam requirements

1 Programming project (informatics: prof. Paoluzzi) (≤ 15)2 Term Paper (biomedical: prof. Ceccanti) (≤ 10)3 Project design and prototype presentations (≤ 5)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 8 / 25

GitHub

GitHub

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 9 / 25

GitHub

SignOn GitHub

GitHub is a web-based hosting service for software development projectsthat use the Git revision control system.

GitHub offers both paid plans for private repositories, and free accounts foropen source projects.

configure git and github (guide)

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Assignments

Assignments

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 11 / 25

Assignments

Enroll to the course !!

send an email to me . . . NOW!

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 12 / 25

Assignments

Projects subjects of 2014

1 Essay (Pre-thesis) on bioinformatics topics at the Mendel Institutewith Dr. Valerio Mazza

2 Import/export of image/graphics/CAD formats to/from LAR format

3 Design and implementation of a dedicated CMS (contentmanagement system) for CRARL (Centro Riferimento AlcologicoRegione Lazio), c/o Policlinico Umberto I

Your choice to be discussed with me (after April, 8)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 13 / 25

Assignments

Projects subjects of 2014

1 Essay (Pre-thesis) on bioinformatics topics at the Mendel Institutewith Dr. Valerio Mazza

2 Import/export of image/graphics/CAD formats to/from LAR format

3 Design and implementation of a dedicated CMS (contentmanagement system) for CRARL (Centro Riferimento AlcologicoRegione Lazio), c/o Policlinico Umberto I

Your choice to be discussed with me (after April, 8)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 13 / 25

Assignments

Projects subjects of 2014

1 Essay (Pre-thesis) on bioinformatics topics at the Mendel Institutewith Dr. Valerio Mazza

2 Import/export of image/graphics/CAD formats to/from LAR format

3 Design and implementation of a dedicated CMS (contentmanagement system) for CRARL (Centro Riferimento AlcologicoRegione Lazio), c/o Policlinico Umberto I

Your choice to be discussed with me (after April, 8)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 13 / 25

Assignments

Projects subjects of 2014

1 Essay (Pre-thesis) on bioinformatics topics at the Mendel Institutewith Dr. Valerio Mazza

2 Import/export of image/graphics/CAD formats to/from LAR format

3 Design and implementation of a dedicated CMS (contentmanagement system) for CRARL (Centro Riferimento AlcologicoRegione Lazio), c/o Policlinico Umberto I

Your choice to be discussed with me (after April, 8)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 13 / 25

Assignments

Projects subjects of 2014

1 Essay (Pre-thesis) on bioinformatics topics at the Mendel Institutewith Dr. Valerio Mazza

2 Import/export of image/graphics/CAD formats to/from LAR format

3 Design and implementation of a dedicated CMS (contentmanagement system) for CRARL (Centro Riferimento AlcologicoRegione Lazio), c/o Policlinico Umberto I

Your choice to be discussed with me (after April, 8)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 13 / 25

Assignments

References

Course syllabus

Principles of Biomedical Informatics, Second Edition

Handbook of Biomedical Informatics

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 14 / 25

Introduction to bioinformatics

Introduction to bioinformatics

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 15 / 25

Introduction to bioinformatics

BioinformaticsOxford English Dictionary, 2001

(Molecular) bio – informatics: bioinformatics isconceptualising biology in terms of molecules (in the sense ofphysical chemistry) and applying ”informatics techniques”(derived from disciplines such as applied maths, computerscience and statistics) to understand and organise theinformation associated with these molecules, on a large scale. Inshort, bioinformatics is a management information system formolecular biology and has many practical applications.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 16 / 25

Introduction to bioinformatics

Bioinformatics Central Dogmastates that DNA is transcribed into RNA, which is then translated into proteins

DNA is composed of 4 nucleotides (guanine, cytosine, adenine, andthymine).

Sets of 3 nucleotides in a string of DNA are called codons.

The 20 amino acids are specified by these codons.

The genetic code is the mapping from codons to amino acids

A gene is a sequence of codons and ”non-coding” sequences that determinewhen the gene is active (expressed).

There are stop and start codons which signal the beginning and end of theprotein coding sequence

Proteins are organic compounds made of amino acids arranged in a linearchain and folded into a globular form.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 17 / 25

Introduction to bioinformatics

Bioinformatics Central Dogmastates that DNA is transcribed into RNA, which is then translated into proteins

DNA is composed of 4 nucleotides (guanine, cytosine, adenine, andthymine).

Sets of 3 nucleotides in a string of DNA are called codons.

The 20 amino acids are specified by these codons.

The genetic code is the mapping from codons to amino acids

A gene is a sequence of codons and ”non-coding” sequences that determinewhen the gene is active (expressed).

There are stop and start codons which signal the beginning and end of theprotein coding sequence

Proteins are organic compounds made of amino acids arranged in a linearchain and folded into a globular form.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 17 / 25

Introduction to bioinformatics

Bioinformatics Central Dogmastates that DNA is transcribed into RNA, which is then translated into proteins

DNA is composed of 4 nucleotides (guanine, cytosine, adenine, andthymine).

Sets of 3 nucleotides in a string of DNA are called codons.

The 20 amino acids are specified by these codons.

The genetic code is the mapping from codons to amino acids

A gene is a sequence of codons and ”non-coding” sequences that determinewhen the gene is active (expressed).

There are stop and start codons which signal the beginning and end of theprotein coding sequence

Proteins are organic compounds made of amino acids arranged in a linearchain and folded into a globular form.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 17 / 25

Introduction to bioinformatics

Bioinformatics Central Dogmastates that DNA is transcribed into RNA, which is then translated into proteins

DNA is composed of 4 nucleotides (guanine, cytosine, adenine, andthymine).

Sets of 3 nucleotides in a string of DNA are called codons.

The 20 amino acids are specified by these codons.

The genetic code is the mapping from codons to amino acids

A gene is a sequence of codons and ”non-coding” sequences that determinewhen the gene is active (expressed).

There are stop and start codons which signal the beginning and end of theprotein coding sequence

Proteins are organic compounds made of amino acids arranged in a linearchain and folded into a globular form.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 17 / 25

Introduction to bioinformatics

Bioinformatics Central Dogmastates that DNA is transcribed into RNA, which is then translated into proteins

DNA is composed of 4 nucleotides (guanine, cytosine, adenine, andthymine).

Sets of 3 nucleotides in a string of DNA are called codons.

The 20 amino acids are specified by these codons.

The genetic code is the mapping from codons to amino acids

A gene is a sequence of codons and ”non-coding” sequences that determinewhen the gene is active (expressed).

There are stop and start codons which signal the beginning and end of theprotein coding sequence

Proteins are organic compounds made of amino acids arranged in a linearchain and folded into a globular form.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 17 / 25

Introduction to bioinformatics

Bioinformatics Central Dogmastates that DNA is transcribed into RNA, which is then translated into proteins

DNA is composed of 4 nucleotides (guanine, cytosine, adenine, andthymine).

Sets of 3 nucleotides in a string of DNA are called codons.

The 20 amino acids are specified by these codons.

The genetic code is the mapping from codons to amino acids

A gene is a sequence of codons and ”non-coding” sequences that determinewhen the gene is active (expressed).

There are stop and start codons which signal the beginning and end of theprotein coding sequence

Proteins are organic compounds made of amino acids arranged in a linearchain and folded into a globular form.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 17 / 25

Introduction to bioinformatics

Bioinformatics Central Dogmastates that DNA is transcribed into RNA, which is then translated into proteins

DNA is composed of 4 nucleotides (guanine, cytosine, adenine, andthymine).

Sets of 3 nucleotides in a string of DNA are called codons.

The 20 amino acids are specified by these codons.

The genetic code is the mapping from codons to amino acids

A gene is a sequence of codons and ”non-coding” sequences that determinewhen the gene is active (expressed).

There are stop and start codons which signal the beginning and end of theprotein coding sequence

Proteins are organic compounds made of amino acids arranged in a linearchain and folded into a globular form.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 17 / 25

Introduction to bioinformatics

Bioinformatics Central Dogmastates that DNA is transcribed into RNA, which is then translated into proteins

DNA is composed of 4 nucleotides (guanine, cytosine, adenine, andthymine).

Sets of 3 nucleotides in a string of DNA are called codons.

The 20 amino acids are specified by these codons.

The genetic code is the mapping from codons to amino acids

A gene is a sequence of codons and ”non-coding” sequences that determinewhen the gene is active (expressed).

There are stop and start codons which signal the beginning and end of theprotein coding sequence

Proteins are organic compounds made of amino acids arranged in a linearchain and folded into a globular form.

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 17 / 25

Introduction to bioinformatics

Bioinformatics Central Dogma

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 18 / 25

Introduction to bioinformatics

Bioinformatics Central DogmaDNA structure

Molecular Biology of the Cell, Fifth Edition ( c© Garland Science 2008)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 19 / 25

Introduction to bioinformatics

Bioinformatics Central DogmaDNA structure

Molecular Biology of the Cell, Fifth Edition ( c© Garland Science 2008)

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 19 / 25

Introduction to bioinformatics

Gene expression process

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 20 / 25

Introduction to bioinformatics

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 21 / 25

Introduction to bioinformatics

Example of PDB (Protein Data Bank) file

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 22 / 25

Introduction to bioinformatics

Example of PDB (Protein Data Bank) file

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 22 / 25

Introduction to bioinformatics

Example of PDB (Protein Data Bank) file

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 23 / 25

Introduction to bioinformatics

Example of PDB (Protein Data Bank) file

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 23 / 25

Introduction to bioinformatics

Example of PDB (Protein Data Bank) file

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 24 / 25

Introduction to bioinformatics

Beyond central dogma: epigenetics

Genetic Science Learning Center – University of UtahWHAT IS EPIGENETICS?

Science 29 October 2010:Vol. 330 no. 6004 p. 611DOI: 10.1126/science.330.6004.611INTRODUCTION TO SPECIAL ISSUEWhat Is Epigenetics?

M. Ceccanti and A. Paoluzzi Biomedical Informatics: Lecture 1 Tue, Mar 4, 2014 25 / 25