Category Archive projects

Byalessandro.fiori

Software Engineer recruitment

Ricerchiamo un Software Engineer da impiegare nel design e nell’implementazione del LAS 2.0: una piattaforma dati Web-based, utilizzata nella ricerca traslazionale sulle patologie oncologiche.

Requisiti:

  • Laurea o Dottorato in Ingegneria Informatica, Informatica o affini
  • Eccellente conoscenza di Python e/o Java
  • Ottima conoscenza dei DBMS relazionali
  • Ottime capacità comunicative
  • Capacità di lavorare indipendentemente e di coordinarsi col team di progetto

Completano il profilo:

  • Conoscenza di MongoDB, Neo4j e del mondo NoSQL
  • Conoscenza delle tecnologie Web semantiche
  • Competenza nel Web-framework Django
  • Competenza nelle tecnologie per il front-end Web (JavaScript / Angular / jQuery / Bootstrap)
  • Pubblicazioni in conferenze e riviste internazionali
  • Esperienza nel modeling 3D e nell’utilizzo di motori di rendering

Il candidato selezionato verrà inserito nel team progettuale del LAS e la sua attività verterà principalmente sui nuovi sviluppi della piattaforma.

Come candidarsi?

Se interessati, si prega di inviare la propria candidatura, comprensiva di (i) CV, (ii) lettera di presentazione ed (iii) eventuali referenze, ai seguenti indirizzi

  • Andrea Bertotti (email: andrea.bertotti@ircc.it)
  • Alessandro Fiori (email: alessandro.fiori@ircc.it)

Ulteriori informazioni sul progetto LAS/LAS 2.0

Il LAS (Laboratory Assistant Suite) è nato nel 2011 e fa parte della classe di software chiamata LIMS (Laboratory Management Information System). Questo tipo di applicativi mira a tracciare, integrare e a rendere fruibile l’informazione generata nei laboratori biomedici. La piattaforma è attualmente funzionante ed assiste quotidianamente i ricercatori nelle attività di laboratorio. L’architettura della piattaforma è modulare. Ogni modulo è deputato alla gestione di differenti procedure sperimentali e dei relativi tipi di dato (es., dati biologici, dati genomici, ecc…), ed è innestato in un framework principale, per permettere l’integrazione dell’informazione in un unico punto di vista centralizzato. Il LAS è basato su un approccio dati multimodello che integra: MySQL, MongoDB e Neo4j. Le interfacce utente sono Web-based e sono state progettate ed implementate per essere fruibili in ambienti ostili, ove è necessario minimizzare le interazioni uomo-macchina per il data entry.

Il progetto LAS 2.0 mira ad estendere la piattaforma attuale per migliorarne la scalabilità di implementazione dei moduli dedicati alla gestione dei nuovi processi di laboratorio. Per questo motivo, il LAS 2.0 è fondato su una base di conoscenza semantica in grado di generalizzare ed armonizzare le pipeline procedurali e di relazionare le relative tipologie di dati sperimentali provenienti da diversi contesti.

 

English version

A fully funded software engineer position is available on the LAS 2.0 project at IRCSS of Candiolo, Italy.

In 2011, IRCSS of Candiolo started a project, named LAS (Laboratory Assistant Suite), addressed to develop a Laboratory Management Information System (LIMS). The 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 LAS 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.

The selected candidate will join the LAS project team and her/his activity will be strongly focused on the development of the LAS 2.0 project. 

Skills & Requirements

Basic skills and requirements:

  • Graduate degree (Masters or PhD) in computer science or a related field
  • Good knowledge of Python and/or Java
  • Good knowledge of DBMSs
  • Excellent communication skills – written and oral
  • Ability to work independently and in team

Additional skills (nice to have’s):

  • Expertise in MongoDB, Neo4j and NoSQL world
  • Expertise in  front-end techs or frameworks: JavaScript / Angular / jQuery, and responsive design competencies: Bootstrap
  • Knowledge of semantic technologies
  • Expertise in Django Web framework
  • Publications in top-level conferences and journals
  • Expertise in 3D Modeling and rendering libraries

Application submission and further details

Please, address your application with (i) CV, (ii) motivation letter and (iii) optional reference letters to:

  • Andrea Bertotti (email: andrea.bertotti@ircc.it)
  • Alessandro Fiori (email: alessandro.fiori@ircc.it)

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.

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