Date post: | 26-May-2015 |
Category: |
Technology |
Upload: | lasircc |
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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
nt a
nd
Priv
ileg
e M
an
ag
er
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