Yearly Archive 2017

Byalessandro.fiori

Data Analysis Visualization

Goals

Innovative approaches to visualize big data obtained by nect generation sequecing

Innovative software environments to explore data mining results

Integrative molecular analyses fro personalized medicine and precision oncology

 

Successful candidates are expected to acquire the following skills:

Database (relational, NoSQL, GraphDB) Bioinformatics
Web Programming (Python, Java, AngularJS) Data mining visualization

 

 

 

We are looking for students seriously determined to increase their skills in a challenging teamwork-oriented environment.
PLACE OF WORK: Politecnico di Torino in collaboration with IRCCS Candiolo
CONTACTS: Andrea Bertotti – andrea.bertotti@ircc.it

Alessandro Fiori – alessandro.fiori@ircc.it

Byalessandro.fiori

Virtual Laboratory

The thesis aims at exploiting computer vision for sensor-based real-time tracking of laboratory activities. The main goal is to develop a prototypic platform for automated monitoring of interactions between users, instruments and experimental materials. A virtual representation of objects and activities is also foreseen to provide intuitive and user-friendly GUIs.

Goals

Biological laboratories need Next Generation LIMS

Computer Vision to improve the efficiency of laboratory data-tracking procedures

Interactive 3D visualization for real time representation of user activities and laboratory workflows

 

Successful candidates are expected to acquire the following skills:

Sensor and optical systems management 3D object recognition
Programming (Python, Java) Motion analysis

 

 

We are looking for students seriously determined to increase their skills in a challenging teamwork-oriented environment.
PLACE OF WORK: Politecnico di Torino in collaboration with IRCCS Candiolo
CONTACTS: Andrea Bertotti – andrea.bertotti@ircc.it

Alessandro Fiori – alessandro.fiori@ircc.it

Byalessandro.fiori

3D Laboratory

This project aims at realizing a virtual representation of life-science working environments based on 3D interactive models. The main goal is to develop a prototypic application for user-friendly management of complex and hierarchical storage systems by means of 3D realistic representation of the physical containers and their interactions.

Goals

Biological laboratories need Next Generation LIMS

Virtual reality to improve graphical user interfaces usability in laboratory information management systems (LIMS)

Interactive 3D visualization to manage instruments and physical supports

 

Successful candidates are expected to acquire the following skills:

Database (relational, NoSQL, GraphDB) 3D models design and rendering
Web design

 

 

We are looking for students seriously determined to increase their skills in a challenging teamwork-oriented environment.
PLACE OF WORK: Politecnico di Torino in collaboration with IRCCS Candiolo
CONTACTS: Andrea Bertotti – andrea.bertotti@ircc.it

Alessandro Fiori – alessandro.fiori@ircc.it

Byalessandro.fiori

Clinical Data Management

The thesis aims at exploiting database and web technologies for tracking and analyzing clinical data . The main goal is to
develop a web-based platform for monitoring clinical information of patients and extracting relevant knowledge.

Goals

Clinical research units need Next Generation CDM

Ontologies to standardize clinical data

Integrative analysis for personalized medicine and precision oncology

 

Successful candidates are expected to acquire the following skills:

Database (relational, NoSQL, GraphDB) Web design
Programming (Python, Java) Statistical data analysis

 

 

We are looking for students seriously determined to increase their skills in a challenging teamwork-oriented environment.
PLACE OF WORK: Politecnico di Torino in collaboration with IRCCS Candiolo
CONTACTS: Andrea Bertotti – andrea.bertotti@ircc.it

Alessandro Fiori – alessandro.fiori@ircc.it

Byalessandro.fiori

Integrative analysis of Translational Cancer Data

Goals

Innovative approaches to integrating biological data by means of semantic technology

Query engine to retrieve and aggregate relevant heterogeneous data

Visualization tools to explore xenograft models and genomic data

 

 

 

 

Successful candidates are expected to acquire the following skills:

Database (relational, NoSQL, GraphDB) Semantic engines
Web design Bioinformatics
Programming (Python, Java)

 

 

We are looking for students seriously determined to increase their skills in a challenging teamwork-oriented environment.
PLACE OF WORK: Politecnico di Torino in collaboration with IRCCS Candiolo
CONTACTS: Andrea Bertotti – andrea.bertotti@ircc.it

Alessandro Fiori – alessandro.fiori@ircc.it

Byalessandro.fiori

Postdoctoral fellowship in Data Modeling for Translational Research

A fully funded postdoctoral position is available on the LAS 2.0 project at Department of Oncological Sciences, University of Torino Medical School, Italy.
Application deadline: There is no fixed deadline, we will continue accepting applications until suitable candidates have been found. You will receive an acknowledgement of your application by email within a week’s time.

In 2011, our department started a project, named LAS, addressed to develop a Laboratory Management Information System (LIMS). The Laboratory Assistant Suite (LAS) platform assists biomedical researchers in a broad variety of laboratory activities. Its modular architecture allows managing different kinds of raw data (e.g., biological, molecular) and tracking experimental procedures. While each LAS module handles specific activities or data types, a broader and uniform framework ensures native integration and coherence among the various system components. User interfaces have been designed to be practical in hostile environments, where researchers should minimize their interactions with the system during data entry procedures (e.g., in sterile conditions).

The LAS 2.0 project aims to extend the current platform to provide more flexibility and customization in defining experimental pipelines, normalize and harmonize general concepts and data models applied to different domains, and maintaining consistency among different data-flows and workflows. The new system will integrate a semantic knowledge base that integrates several ontologies covering different domains. The architecture will include reasoning tools and different NOSQL databases (i.e., graph and document databases) to improve the flexibility of the platform.

Qualifications

The postdoc researcher will be members of the LAS project team. More specifically, the researcher will participate in relevant research and development activities connected to the project. For this reason, successful candidates are expected to perform excellent research within Knowledge Bases, Database Modeling, Software Engineering, or related areas. We primarily seek candidates who have a PhD in ICT, with specialization related to the above-mentioned areas. Besides personal qualities and the ability to work in team, we will prioritize candidates based on the following criteria:

  • Strong publication record, with publications in top-level conferences and journals
  • Excellent communication skills – written and oral
  • Ability to work independently and in team

Proficiency in the English language should be documented.

Application submission

Submit your application with CV to
Andrea Bertotti (email: andrea.bertotti@ircc.it), and
Alessandro Fiori (email: alessandro.fiori@ircc.it)

Byalessandro.fiori

Knowledge Base-driven Laboratory Management System

When building software systems for describing and managing laboratory experimental processes, the wide range of possible investigations presents several challenges. Different levels of representation complexity and granularity and various descriptive terms can be used to describe the processes of interest.


To govern such dynamism and data heterogeneity, our research group is developing an ambitious project that includes the design of a Knowledge Base, a system to represent facts about the world, and an inference engine to reason about those facts, deduce new knowledge and highlight inconsistencies by means of rules.

 

 

Successful candidates are expected to acquire the following skills:

Programming (Java, Python) Knowledge and content management
NoSQL Database Expertise with semantic technologies and
Natural Language Processing
Ontologies (OWL, Protegé editor)

 

We are looking for students seriously determined to increase their skills in a challenging teamwork-oriented environment.
PLACE OF WORK: Politecnico di Torino in collaboration with IRCCS Candiolo
CONTACTS: Andrea Bertotti – andrea.bertotti@ircc.it

Alessandro Fiori – alessandro.fiori@ircc.it

ByAndrea Mignone

Laboratory Assistant Suite

A superheroic platform for the lab data management

ByAndrea Mignone

Read more about LAS

Discover the platform capabilities

ByAndrea Mignone

Tracking of genomic data

Track and manage genomic information