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STOCKS

STOCKS: Solution for lab stocks management

 

Try STOCKS on our demo server (login: demo/demo)

EMBL Users: You can start using the EMBL STOCKS immediately using your EMBL credentials (needs VPN for external access).

=> Contact us if you need new stock types (fly lines, primers ...) or want to customize existing ones (add new fields, new vocabulary in select options)

Quick Overview

STOCKS is a free (soon-to-be open-source) web application for Research Data Management. It can be deployed for a single group or a whole institute.

It offers

  • An Electronic Lab Notebook (ELN) to record your daily notes featuring digital timestamping to guaranty intellectual property
  • Lab Collections/Inventory Module to easily manage and share your lab collections (plasmids, chemicals, etc.), instruments (microscopes, freezers, etc.) or animal collections (fly lines, mouse strains, etc.).
  • An associated Order Module to track when items were ordered
  • Protocol Module to readily version and share the protocols used daily in your group or institute.
  • Sample Module to track and manage all your samples, their lineage (parent-child relationships) and their connections to your experiments (lab notes) and assays
  • Dataset Module to manage both assay-generated raw (e.g. NGS) and derived datasets; track which assay and instrument they derive from, their lineage up to the samples initially used and the ELN notes.
  • Controlled Vocabulary Module to ensure accurate and valid terms are used for later submission to public repositories (e.g. ENA) and unify how users annotate items.

and also features

  • An Advanced Permission System that allows you to share and decide who can view and/or edit your collection items, projects and ELN notes
  • An Application Programming Interface (API) that enables programmers to interact programmatically with STOCKS. This allows e.g. to transfer and register datasets automatically from data-producing facilities to STOCKS to ensure full traceability and minimize user data manipulation.
  • Integration with Galaxy (e.g. to readily send data files to Galaxy)
  • An Integrated Online Editor using LibreOffice Online to readily edit and share documents. 
  • Data export to allow e.g. excel spreadsheets or PDF documents export and prevent vendor lock-in issues

 

Roadmap

  • STOCKS currently support NGS data storage. We are currently looking into supporting more data generating assays like proteomics, metabolomics and imaging. 
  • Interoperability with analysis platforms: our goal is to allow export of datasets (and metadata) to platforms like Galaxy and automatic re-import of generated datasets. 
  • Open Science: allowing to expose your lab notebooks (as an external read-only web site) together with data public release 
  • Exposing datasets through custom, project-based, web sites where raw and processed datasets can be discovered and downloaded by the community 

Feature List

Global features

  • Free Text and Advanced search functionality available on all list pages.
  • Customizable display of all tables i.e. item per page, columns to show, column order... Different display options can be saved for each STOCKS type.
  • Controlled vocabulary whenever applicable. Tell us if you are missing a term in a drop-down.
  • Exact stock locations can be provided for all STOCKS items in lab collections & samples
  • Attach documents and leave notes on every STOCKS item 
  • Rich permission system lets you decide who can see & edit your entries 

Lab Collections Management & Customization

  • Management for following lab collection types:
    • Consumables: items that you buy and use in your experiments (ELN)
    • Specimen: your living stock i.e. from which you derive samples
    • Equipment: devices, instruments, and storage equipment (e.g. freezers)
  • New consumable, specimen or equipment sub-types can be easily added, with all desired custom fields. Simply get in touch with us.
  • The Order module lets you:
    • track when stocks have been ordered e.g. “How frequently and where does my stock was ordered in the past?"
    • store the prices, ordered quantities and ordered item recipients
    • store the SAP shopping cart ID * notify users per email upon receiving of their order(s) by a single click

Protocol Module Details

  • Define protocols as Word-like formatted text including pictures and tables 
  • Maintain the parent-child relationship between versioned protocols
  • Classify protocols into protocol types
  • Share with your group or everyone

Sample Module Details

  • Keep track of your valuable samples and their location
  • Derive samples from your Specimen collections to inherit specimen properties (eg annotations)
  • Full support of complex sample lineage: parent-child relationships, including merge & split
  • Link to the protocols used to produce the samples, even without using the ELN module
  • Define how samples are consumed by e.g. sequencing assays

ELN

  • Record your daily Experiments as Word-like formatted text including pictures and tables 
  • Use Protocol as a template to create new experiments, then only edits the changes or fill in empty values! 
  • Attach important documents to your experiments
  • Define links to used/produced samples & key lab collections
  • Export your experiment as a PDF or a complete archive 
  • Freeze & digitally timestamp your experiments to later prove when the work was done (IP)

Dataset Management

Dry lab scientists can access fully described and annotated raw datasets, files and file versions. Processed files created by the computational analysis of raw data, as well as any publicly available dataset, can be registered and organised. In STOCKS, relevant parent-child relationships is recorded when one entity derives from another and this is also true for data files handled within the system.

When a project wraps up, such extensive record of the analysis chain from raw material, to raw data, to publication material, greatly simplifies the publication process in particular when authors have already left the lab.