LaboratoryAssistant

Suite

Starting May 2011, LAS stems from the joined efforts of IRCC and the Politecnico of Torino

Players

IRCC contribution

•Strategy

•Working- and Data-flow analysis

•User interface definition

•On-site implementation

POLITO contribution

•Database & Data warehouse

•Analytical tools & software features

•IT

Goals

Structured data management

•Samples data (biobank)

•Biological data (xenos and cell lines)

•Molecular data (instruments)

•Public data (open access databases)

Integrative analysis management

•Complex queries across multiple databases (including clinical annotations)

•Analysis tools

•Annotations

Features

Data Entry• Real-time• Time saving• User friendly• Error proof

Data Analysis• Integrative• Reproducible• Intuitive• No programming skills required

Technical Specs

• Web-based

• Ad-hoc GUIs

• Relational and NOSQL Databases

• Distributed

• Audit trail

• A mnemonic code (GenID) intrisically represents the most critical attributes of the

main biological entities

Genealogy ID

Features

• Unique• Intrinsic to key biological entities• Encodes relevant information regarding the history of the entity • Automatically generated through formal rules

CRC 0001 LM X 0A 01 001 TUM RL0100

Collection type(tumor type, eg colorectal)

Collection Event(sequencial)

Tissue type(eg liver metastasis)

Vector type(eg xeno, original human or cell line)

Lineage(eg tracks the line generation event)

Passage(n° of generations

ex-vivo)

Mouse ID(individual mouse

number)

XENOPATIENT ALIQUOT

Explanted Tissue

(eg tumor, lung, liver, etc.)

Aliquot type(eg RNAlater)

Aliquot ID(individual aliquot

number)

Data Flow

Operation

Tissue Aliquots

Derived Aliquots Storage

BIOBANKING

EXPERIMENTS

Molecular Experiments

Implants

Mouse

Explants

XENOPATIENTS

Treatments

Measurements

ImagesNext Generation Sequecing

LAS data tracking system

Sample Containers

Surgical Specimens

LAS ALIQUOTs

Mice

LAS XENOs

BIOLOGICAL DATA

LAS ALIQUOTs

MOLECULAR DATA

TRANSFORMATION EVENTS

EXPANSION EVENTSBiobank

Storage Xeno

Facilities

Integrative analyses

LAS facts&numbers

LAS manages (starting April 2012):

• 622 surgical samples collection

• 7158 mice

• 6895 implanted xenografts

• 4790 explanted xenografts

• 18537 measures (digital caliper)

• 1656 mice treated with 44 different

protocols&schedules

• 51131 archived aliquots

• 3530 derivation events (eg DNA extraction)

Cell lines management

LAS modules

Pathology Animal facility

Animal models

Xeno management

Biobank managemen

t

Storage managemen

t

working

Integrative query module

uArray managemen

t

SangerSeq managemen

t

Animal imaging

Public data miner

RT-PCR management

Microscopy

FACS &Beaming

General facilities manager

Integrative analysis module

advanced developme

nt

early developme

ntscheduled

STATUS

intermediate

development

Clinical data miner

Accou

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nd

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Current Functionalities

Biobank

• Sample collection tracking

• Aliquots Exchange/Split/Usage tracking

• Support to derivation processes (protocols,

QC/QA)

• Consumables stock usage (Kits)

Xenopatients

• Mice life cycle tracking

• Surgery practices tracking

• Tumor growth tracking

• Treatment protocols

• Support to decision making process for

experiments

Storage

• Management of containers

• Tracking archive process

Query

• Definition of complex queries

• Integration of heterogeneous data

• Exploration of genealogy trees

Analysis

• Data mining analyses

• Computation of aggregated data

• Plot of data statistics

People

• IRCC (contributors&users)

• Eugenia Zanella• Giorgia Migliardi• Francesca Cottino• Francesco Galimi• Michela Buscarino• Carlo Zanon• Gabriele Picco• Roberta Porporato• Daniela Cantarella• Tommaso Renzulli• Enzo Medico

• POLITO (developers)

staff• Alessandro Fiori (coordinator)

• Alberto Grand• Piero Alberto• Emanuele Geda

students• Marco Alaimo• Francesco Brundu• Maria Cabiati• Stefania Mellai• Raffaele Passanati• Domenico Schioppa

MilestonesThe project is implemented through three steps:

Phase I - Biobanking & Xenopatients management• Storage• Aliquots (tissues & derivatives)• Transformation processes• Mice• In Vivo experiments

Phase II - General facilities management• uArrays• Sanger sequencing• RT-PCR• FACS• Animal Facility (?)

Phase III - General purpose data management• In vitro experiments• Imaging• Analytical tools• NextGenSeq data management (in collaboration with informatics)• Mouse models• Clinical data integration

Biobanking Module

Xenografts Module

Query Module