THREE-DIMENSIONAL MODELING

Course objectives

Bioinformatics is the discipline that deals with the analysis and attribution of biological significance to the large amount of biomolecular data available today and represents an essential tool in the field of basic biochemical, biological-molecular, biomedical and research activities. biotechnology. The Bioinformatics Laboratory course aims to introduce the biology student to the use of the most common computational tools nowadays used in bioinformatic sequence analyzes and structures of both proteins and nucleic acids and the acquisition of knowledge on their functioning . Students who pass the exam will have acquired: a) knowledge and ability to understand the nature of biomolecular data the logical basis of the most common bioinformatic data analysis programs ability to process simple bioinformatic analyzes of data in the application and research fields b) ability to apply knowledge and understanding in the rational and effective use of the most common bioinformatics tools in the identification of the instrument suitable for the solution of a specific biological problem know how to plan the transfer of theoretical results to experimental practice c) autonomy of judgment know how to identify the limits of application of bioinformatics tools know how to interpret and critically apply the results obtained d) communication skills know how to illustrate the logic used to identify the bioinformatics tool suitable for solving a biological problem know how to communicate and explain the meaning of the facts during an oral interview e) learning ability the basic knowledge to progress autonomously in learning the use and operation of more advanced bioinformatics tools

Channel 1
ALLEGRA VIA Lecturers' profile

Program - Frequency - Exams

Course program
Module 2 of the Bioinformatics Laboratory course is organised into five thematic modules. The detailed content of each module is available on the course website at https://sites.google.com/uniroma1.it/laboratoriodibioinformatica/home and summarised below: Module 1: Genomics: what is it? how does it come about? Useful online resources. - Review of biology concepts needed to understand genomics - Introduction to genomic bioinformatics - Genomics, transcriptomics, proteomics, metabolomics - Useful online resources: NCBI Gene, Ensembl, GENCODE, NCBI PubMed, miRBase, miRTarBase, g:Profile, BioMart Module 2: ABC of shell scripting - The Linux command line (Terminal) - Bash language commands for - navigate the filesystem - create/edit and save a plain text file - execute a program - check the size of a text file - edit a text file - copy, delete and move files and folders - process text data - search for words in a text file Module 3: Differential expression analysis: purposes and modalitiesGEO (Gene Expression Omnibus) - Purpose of a differential expression analysis - How to assay gene expression on a genome-wide scale - Microarrays - RNA-Seq - Data repository: GEO (Gene Expression Omnibus), GEO2R, microarrays Module 4: Genome exploration: UCSC genome browser - Navigating genomic information: UCSC Genome Browser and Ensembl BioMart Module 5: Analysis of networks in genomics: application examples - Molecular interaction networks - Integrating gene expression data into a network of interactions - Cytoscape: open source software platform for the visualisation of complex networks and their integration with annotation data.
Prerequisites
Basic knowledge of fundamental concepts of molecular biology, in particular: DNA, RNA, genome, transcriptome, proteome, transcription, translation, expression and gene regulation.
Books
All the essential learning material (Lectures, Tutorial guides and supporting files) will be provided to the students on the module’s webpage at: https://sites.google.com/uniroma1.it/laboratoriodibioinformatica/home. No specific text book is required.
Frequency
Attendance is not compulsory but strongly recommended: the module has a very important practical component and it would be very difficult to pass the exam without having attended the course.
Exam mode
Successful completion of this module will be assessed by a practical test and a short oral interview commenting on the test given Both in the oral and practical test, the problems to be solved will be on topics covered in this course, according to the type of small problems, challenges and questions that will be gradually encountered in the course of the activities in class.
Lesson mode
The course includes lectures and computer-based exercises. Through lectures, students learn the fundamental knowledge of genomic bioinformatics. The exercises are aimed at the acquisition of computational skills. By solving simple problems and exercises, students learn how to apply bioinformatics knowledge and skills to solving biological problems and answer questions in the context of genomics.
ALLEGRA VIA Lecturers' profile

Program - Frequency - Exams

Course program
Module 2 of the Bioinformatics Laboratory course is organised into five thematic modules. The detailed content of each module is available on the course website at https://sites.google.com/uniroma1.it/laboratoriodibioinformatica/home and summarised below: Module 1: Genomics: what is it? how does it come about? Useful online resources. - Review of biology concepts needed to understand genomics - Introduction to genomic bioinformatics - Genomics, transcriptomics, proteomics, metabolomics - Useful online resources: NCBI Gene, Ensembl, GENCODE, NCBI PubMed, miRBase, miRTarBase, g:Profile, BioMart Module 2: ABC of shell scripting - The Linux command line (Terminal) - Bash language commands for - navigate the filesystem - create/edit and save a plain text file - execute a program - check the size of a text file - edit a text file - copy, delete and move files and folders - process text data - search for words in a text file Module 3: Differential expression analysis: purposes and modalitiesGEO (Gene Expression Omnibus) - Purpose of a differential expression analysis - How to assay gene expression on a genome-wide scale - Microarrays - RNA-Seq - Data repository: GEO (Gene Expression Omnibus), GEO2R, microarrays Module 4: Genome exploration: UCSC genome browser - Navigating genomic information: UCSC Genome Browser and Ensembl BioMart Module 5: Analysis of networks in genomics: application examples - Molecular interaction networks - Integrating gene expression data into a network of interactions - Cytoscape: open source software platform for the visualisation of complex networks and their integration with annotation data.
Prerequisites
Basic knowledge of fundamental concepts of molecular biology, in particular: DNA, RNA, genome, transcriptome, proteome, transcription, translation, expression and gene regulation.
Books
All the essential learning material (Lectures, Tutorial guides and supporting files) will be provided to the students on the module’s webpage at: https://sites.google.com/uniroma1.it/laboratoriodibioinformatica/home. No specific text book is required.
Frequency
Attendance is not compulsory but strongly recommended: the module has a very important practical component and it would be very difficult to pass the exam without having attended the course.
Exam mode
Successful completion of this module will be assessed by a practical test and a short oral interview commenting on the test given Both in the oral and practical test, the problems to be solved will be on topics covered in this course, according to the type of small problems, challenges and questions that will be gradually encountered in the course of the activities in class.
Lesson mode
The course includes lectures and computer-based exercises. Through lectures, students learn the fundamental knowledge of genomic bioinformatics. The exercises are aimed at the acquisition of computational skills. By solving simple problems and exercises, students learn how to apply bioinformatics knowledge and skills to solving biological problems and answer questions in the context of genomics.
  • Academic year2025/2026
  • CourseBiology
  • CurriculumBiotecnologico cellulare
  • Year3rd year
  • Semester2nd semester
  • SSDBIO/10
  • CFU3