Currently, the demand for experts in biomedical computing (medical informatics, bioinformatics, biomedical data science, and in silico medicine) exceeds the availability of newly graduated in these disciplines. The RE-TRAIN-ME project aims to provide post-degree training in biomedical computing to people with a master's degree in math, physics, chemistry, biology, engineering, etc. but no specific training in biomedical computing.
The call is open to everyone with a total of five years of university education, typically a three years bachelor's and a two years master’s, in biology, biotechnology, pharmacy, physics, informatics, engineering, mathematics, human and veterinary medicine, chemistry, materials science, astronomy, natural sciences, statistical science (for Italians see “classi di laurea magistrale”).
Applicants must submit their application online, including a curriculum vitae in Europass CV format. A panel of experts will rank the applicants based on their CVs and preference for the four application areas: medical informatics, bioinformatics, biomedical data science, and in silico medicine.
A maximum number of applicants will be admitted to the first part of the programme. This number will be for each year equal to twice the number of available scholarships and, in any case, no more than 30.
For the year 2023/24, the four participating organisations will fund a total of ten (10) scholarships (or equivalent form of paid contract); thus, the maximum number of participants for the year 2023/24 is 20. Among them, up to ten will be offered a scholarship for the period 1-2-2024 to 30-9-2024 by the following organisations:
Applications must be submitted before Sept 10th, 2023.
The applicants admitted to the programme will follow three mandatory online courses (Elements of Informatics, Programming, and Elements of Biomedical Computing). The courses will start on 25/9/2023 and will end on 15/12/2023. Attendance will be monitored, and every participant is expected to attend 90% of the lectures or be expelled by the programme. Below we provide a detailed list of topics taught in each module, and the tentative calendar of the lectures.
Elements of informatics will provide core training in computer science, whereas programming will cover Bash, Python, and R programming languages. In the module Elements of Biomedical Computing, various experts will introduce the four application areas: medical informatics, bioinformatics, biomedical data science, and in silico medicine.
At the end of this first online training period, each participant will decide whether to stop or apply for one of the scholarships linked to each of the four application areas. This second selection will be made through interviews in January 2024. Those who are not selected for a scholarship, or decide not to apply, will receive an attendance certificate.
Those selected for the scholarship in one of the application areas will continue to receive in-person training on that subject and start hands-on training on an exemplary problem until 24/09/2024, for 12 months in total.
Theoretical bases: Von Neumann architecture, Turing machine; Hardware: CPU, RAM, storage, input, outputs; Hardware: GPU, bus, network adapters; Networks: From Ethernet to the Internet; Operating system and file systems; Compilers and programming environments; Database; Cloud computing; Time-sharing computer e HPC; Elements of information theory.
Introduction to the Unix Shell, Files and Directories; Pipes and filters e cycles; Scripting and finding things; Introduction to databases and SQL; Data manipulation; Introduction to the language and installation; Variable types, string formatting, containers, and operations; Cycles and conditions, functions, input/output; Introspection and modules, Classes - object-oriented programming; Error handling, Standard library, Scientific modules.
Introduction to biomedical computing; Data, information, knowledge, wisdom; Introduction to Data Science; Fundamentals of statistics; Types of data in healthcare; Electronic medical record; Introduction to Molecular biology; Comparing sequences; Introduction to in silico medicine; Biophysical models.
Types of data in healthcare; Electronic medical record; Bioimages e DICOM; Biosignals; Clinical data: HL7 and CDA; Coding systems: SNOMED, ICD, LOINC, SDO, DRG; Security to protect clinical data; Electronic health records; Telemedicine; Digital Twins.
Introduction to Data Science; Fundamentals of Statistics; Data Visualisation; Data Mining; Contingency Tables; Logistic Regression; Introduction to Probability and Information Theory; Introduction to Machine Learning.
Analysis of Exome sequencing data for clinical application; Introduction to long-read sequencing applications and analyses; Getting closer to the phenotype: proteomics and metabolomics; The impact of the "Genomic era” on daily life.
Introduction to in silico medicine; Biophysical models: finite element methods; Biophysical models: condensed parameter methods; Finite state machines: agent-based models; Stochastic modelling; The credibility of predictive models; Clinical applications of patient-specific models.
|1||Monday||25/9/2023||10:00-12:00||Introduction to Computer Science||Theoretical bases: Von Neumann architecture, Turing machine|
|2||Tuesday||26/9/2023||10:00-12:00||Programming||Bash - Introduction to the Unix Shell, Files and Directories|
|3||Wednesday||27/9/2023||10:00-12:00||Introduction to Biomedical Computing||Introduction to biomedical computing|
|4||Monday||2/10/2023||10:00-12:00||Introduction to Computer Science||Hardware: CPU, RAM, storage, input, outputs|
|5||Tuesday||3/10/2023||10:00-12:00||Programming||Bash - Pipes and filters e cycles, Scripting and finding things|
|6||Wednesday||4/10/2023||10:00-12:00||Introduction to Biomedical Computing||Data, information, knowledge, wisdom|
|7||Monday||9/10/2023||10:00-12:00||Introduction to Computer Science||Hardware: GPU, bus, network adapters|
|8||Tuesday||10/10/2023||10:00-12:00||Programming||SQL - Introduction to databases and SQL|
|9||Wednesday||11/10/2023||10:00-12:00||Introduction to Biomedical Computing||Fundamentals of statistics|
|10||Monday||16/10/2023||10:00-12:00||Introduction to Computer Science||Networks: From Ethernet to the Internet|
|11||Tuesday||17/10/2023||10:00-12:00||Programming||SQL - Data manipulation|
|12||Wednesday||18/10/2023||10:00-12:00||Introduction to Biomedical Computing||Introduction to Data Analytics|
|13||Monday||23/10/2023||10:00-12:00||Introduction to Computer Science||Operating system and file systems|
|14||Tuesday||24/10/2023||10:00-12:00||Programming||Python - Introduction to the language and installation, variable types and operations|
|15||Wednesday||25/10/2023||10:00-12:00||Introduction to Biomedical Computing||Types of data in healthcare|
|16||Monday||30/10/2023||10:00-12:00||Introduction to Computer Science||Compilers and programming environments|
|17||Tuesday||31/10/2023||10:00-12:00||Programming||Python - string formatting, containers, control flow|
|18||Wednesday||1/11/2023||10:00-12:00||Introduction to Biomedical Computing||Electronic medical record|
|19||Monday||6/11/2023||10:00-12:00||Introduction to Computer Science||Database|
|20||Tuesday||7/11/2023||10:00-12:00||Programming||Python - Functions, input/output, error handling|
|21||Wednesday||8/11/2023||10:00-12:00||Introduction to Biomedical Computing||Introduction to molecular biology|
|22||Monday||13/11/2023||10:00-12:00||Introduction to Computer Science||Cloud computing|
|23||Tuesday||14/11/2023||10:00-12:00||Programming||Python - Introspection and modules, Classes - object-oriented programming|
|24||Wednesday||15/11/2023||10:00-12:00||Introduction to Biomedical Computing||Comparing sequences|
|25||Monday||20/11/2023||10:00-12:00||Introduction to Computer Science||Time-sharing computer e HPC|
|26||Tuesday||21/11/2023||10:00-12:00||Programming||Python - Standard library, Scientific modules (I)|
|27||Wednesday||22/11/2023||10:00-12:00||Introduction to Biomedical Computing||Introduction to in silico medicine|
|28||Monday||27/11/2023||10:00-12:00||Introduction to Computer Science||Elements of information theory|
|29||Tuesday||28/11/2023||10:00-12:00||Programming||Python - Scientific modules (II)|
|30||Wednesday||29/11/2023||10:00-12:00||Introduction to Biomedical Computing||Biophysical models|
|31||Tuesday||27/1/2024||10:00-12:00||Health Data Science||Introduction to Data Science|
|32||Monday||4/2/2024||10:00-12:00||Medical Informatics||Types of data in healthcare|
|33||Wednesday||6/2/2024||10:00-12:00||Bioinformatics||Analysis of Exome sequencing data for clinical application 1|
|34||Thursday||7/2/2024||10:00-12:00||In Silico Medicine||Introduction to in silico medicine|
|35||Monday||13/2/2024||10:00-12:00||Medical Informatics||Electronic medical record|
|36||Tuesday||14/2/2024||10:00-12:00||Health Data Science||Fundamentals of statistics, contingency tables, logistic regression|
|37||Wednesday||15/2/2024||10:00-12:00||Bioinformatics||Analysis of Exome sequencing data for clinical application 2|
|38||Thursday||16/2/2024||10:00-12:00||In Silico Medicine||Biophysical models: finite element methods part 1|
|39||Tuesday||23/2/2024||10:00-12:00||Health Data Science||Data Visualisation|
|40||Wednesday||24/2/2024||10:00-12:00||Bioinformatics||Analysis of Exome sequencing data for clinical application 3|
|41||Thursday||25/2/2024||10:00-12:00||In Silico Medicine||Biophysical models: finite element methods part 2|
|43||Tuesday||27/02/2024||10:00-12:00||Health Data Science||Model uncertainty quantification|
|44||Tuesday||3/3/2024||10:00-12:00||Health Data Science||Model uncertainty quantification|
|45||Wednesday||4/3/2024||10:00-12:00||Bioinformatics||Analysis of Exome sequencing data for clinical application 4|
|46||Thursday||5/3/2024||10:00-12:00||In Silico Medicine||Biophysical models: condensed parameter methods part 1|
|47||Monday||11/3/2024||10:00-12:00||Medical Informatics||Clinical data: HL7 and CDA|
|48||Tuesday||12/3/2024||10:00-12:00||Health Data Science||Deep Learning 1|
|49||Wednesday||13/3/2024||10:00-12:00||Bioinformatics||Introduction to long-read sequencing applications and analyses 1|
|50||Thursday||14/3/2024||10:00-12:00||In Silico Medicine||Biophysical models: condensed parameter methods part 2|
|51||Monday||20/3/2024||10:00-12:00||Medical Informatics||Coding systems: SNOMED, ICD, LOINC, SDO, DRG|
|52||Tuesday||21/3/2024||10:00-12:00||Health Data Science||Deep Learning 2|
|53||Wednesday||22/3/2024||10:00-12:00||Bioinformatics||Introduction to long-read sequencing applications and analyses 2|
|54||Thursday||23/3/2024||10:00-12:00||In Silico Medicine||Finite state machines: agent-based models part 1|
|55||Monday||29/3/2024||10:00-12:00||Medical Informatics||Security to protect clinical data|
|56||Tuesday||30/3/2024||10:00-12:00||Health Data Science||Introduction to probability and information theory|
|57||Wednesday||31/3/2024||10:00-12:00||Bioinformatics||Introduction to long-read sequencing applications and analyses 3|
|58||Thursday||1/4/2024||10:00-12:00||In Silico Medicine||Finite state machines: agent-based models part 2|
|59||Monday||7/4/2024||10:00-12:00||Medical Informatics||Electronic health records|
|60||Tuesday||8/4/2024||10:00-12:00||Health Data Science||Introduction to Machine Learning 1|
|61||Wednesday||9/4/2024||10:00-12:00||Bioinformatics||Getting closer to the phenotype: proteomics and metabolomics|
|62||Thursday||10/4/2024||10:00-12:00||In Silico Medicine||Stochastic modelling|
|64||Tuesday||17/4/2024||10:00-12:00||Health Data Science||Introduction to Machine Learning 2|
|65||Wednesday||18/4/2024||10:00-12:00||Bioinformatics||The impact of the "Genomic era” on daily life 1|
|66||Thursday||19/4/2024||10:00-12:00||In Silico Medicine||The credibility of predictive models|
|67||Monday||25/4/2024||10:00-12:00||Medical Informatics||Digital Twins|
|68||Tuesday||26/4/2024||10:00-12:00||Health Data Science||Introduction to Machine Learning 3|
|69||Wednesday||27/4/2024||10:00-12:00||Bioinformatics||The impact of the "Genomic era” on daily life 2|
|70||Thursday||28/4/2024||10:00-12:00||In Silico Medicine||Clinical applications of patient-specific models|