Section A - Summary
What is Scispot?
Scispot is a modern alternative ELN (Electronic Lab Notebook) & LIMS (Lab Information Management System) that goes beyond traditional lab notebooks and Lab Information Management Systems. Think of Scispot as a data infrastructure that lets you easily create your proprietary lab data. You can use Scispot's graph database and knowledge graph to easily search and discover your data. You can also make your data F.A.I.R (Findable, Accessible, Interoperable, Reusable) using Scispot.
Official Term | Definition | Computing Analogy |
Scispot | A data infrastructure integrating ELN, LIMS, analytics, and automation for lab management, ensuring FAIR data, compliance, and QC checks. | Operating system for managing lab data and workflows. |
Labsheets | Structured databases for managing scientific data (e.g., inventory, samples, orders), supporting barcode tracking, API integration, custom views, and ID column types (Automatic, UUID, ID). | Spreadsheet or relational database for data organization. |
Labspaces | Collaborative folders for organizing experiments, protocols, and documentation, supporting multi-user editing and customizable workflows. | Document management system or collaborative workspace. |
alt-ELN (aka Labspaces) | Scispot’s Electronic Lab Notebook for recording and sharing experimental data, integrated with Labsheets and Template Library. | Digital notebook or content management system. |
alt-LIMS | System for managing lab operations, tracking samples, and ensuring data integrity, customizable via no-code interfaces. | Database management system for lab operations. |
Scibot | AI assistant for natural language interaction, searches, and task automation within Scispot. | Virtual assistant or chatbot. |
Labflows | A lab automation solution for managing orders, sample registration, working samples, tests, and report generation in regulated labs. | Workflow automation tool (e.g., Zapier) for lab processes. |
Manifests | Assay plates or storage boxes (e.g., 96/384-well plates, 10x10 boxes) for tracking samples, with details like well layout and sample types. | Inventory management system for physical lab assets. |
Manifest Templates | Reusable formats for creating manifests, ensuring consistency in plate/box layouts, stored in the Template Library. | Template engine for standardized data structures. |
Location Manager | Tool for tracking and visualizing the physical locations of samples, compounds, and manifests in lab storage (e.g., freezers, racks). | Asset tracking system or geographic information system. |
Knowledge Graph | AI-driven tool for visually searching and discovering data across Scispot’s apps, enhancing data findability. | Graph database or search engine for data relationships. |
App Store | Platform for integrating Scispot with third-party apps and native extensions (e.g., LabSQL, Sequence Designer). | Application marketplace or plugin ecosystem. |
Jupyter Hub | Integration with Jupyter Notebook to access and analyze lab data stored in Scispot. | Data science platform for computational analysis. |
Labsheets: Scientific databases to store inventory, equipment, compounds, sample metadata, and data. You can create Labsheets from scratch or leverage existing templates that Scispot offers.
Official Term | Definition |
Samples | Physical specimens for testing, linked to orders with unique identifiers for tracking in Labsheets or Manifests. |
Working Samples | Aliquots or derivatives created from parent samples for testing, with unique identifiers and links to parent samples and orders. |
Batch | A group of working samples processed together, with a unique identifier for tracking in Labflows. |
Automatic ID | An auto-incrementing identifier for Labsheet entries, with customizable prefix/suffix and automatic barcode generation. |
UUID | A universally unique identifier automatically generated for Labsheet entries, ensuring global uniqueness across systems. |
Manual ID | A user-defined identifier for Labsheet entries, allowing full customization to align with internal naming conventions. |
Reagent | A substance used in reactions, tracked in Labsheets and linked to Location Manager for inventory control. |
Folders | Containers within Labsheets to group Labsheets by project or workflow. |
Labsheet Templates | Pre-designed Labsheet configurations in Scispot for specific research needs (e.g., Microbial Strain Library, ELISA Data), with standard fields for data management. |
Labsheet Merge | A Scispot feature to combine data from multiple Labsheets into a single Labsheet, enabling integrated analysis with synchronization options. |
Labsheet Columns |
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Free Text Column | A Labsheet column for entering unrestricted text data, used for manual input per row. |
Date Column | A Labsheet column for storing dates in standard formats (e.g., MM/DD/YYYY or DD/MM/YYYY). |
List Column | A Labsheet column for creating dropdown menus with predefined options, stored as a reference array. |
Number Column | A Labsheet column for storing numeric values, including decimals or exponentials, with formula support. |
Checkbox Column | A Labsheet column for binary true/false values, used for simple checkbox inputs. |
Image Column | A Labsheet column for embedding and visualizing images (e.g., .tiff, .png, .jpeg), stored in AWS S3. |
Created By Column | A read-only Labsheet column capturing the user details of who created a row, generated by the system. |
Creation Date Column | A read-only Labsheet column recording the date a row is added to a Labsheet, generated by the system. |
Files Column | A Labsheet column for uploading files (e.g., PDF, Excel, Word, CSV) via the GUI, not currently supported by APIs. |
Quantity Column | A Labsheet column that records the amount of a sample or compound, required for creating aliquots or derivatives. |
Quantity Left Column | A read-only Labsheet column for tracking the remaining amount of a sample or compound, used in inventory automation and integrations. |
Quantity Consumed Column | A read-only Labsheet column for tracking the consumed amount of a sample or compound, used in inventory automation and integrations. |
Unit Column | A Labsheet column for selecting units (e.g., millilitres, centimetres) associated with items, using a list format. |
Price Per Unit Column | A Labsheet column that automatically calculates the price per unit for items, using a formulated approach. |
Location Column | A Labsheet column that displays the physical location of an item in the Location Manager. |
Sequence Data Column | A Labsheet column for uploading and visualizing DNA/RNA/amino acid sequences in formats like FASTA, .GB, or .DNA. |
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Sequence Editor | A Scispot tool for designing and managing DNA, RNA, or protein sequences, integrated with Labsheets and Labspaces. |
Chem Data Column | A Labsheet column for uploading, designing, or visualizing chemical structures (e.g., SMILES, MOL, InChi) and checking stereochemical properties. |
Chem Editor | A Scispot tool to create and edit chemical structures, integrated with Labsheets and Labspaces |
Status Column | A Labsheet column for selecting predefined status options, similar to a List Column with dropdown menus, used to track the state of samples or processes. |
Formula Column | A Labsheet column that supports automated calculations using numeric data, enabling dynamic computations for values like quantities or prices. |
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Aliquots/Derivatives | Portions of samples or compounds created for long-term storage or working solutions, with automated or customized IDs. |
Create Children | A Labsheet feature to generate aliquots or derivatives from selected samples or compounds, specifying quantity and ID type. |
Parent Column | A Labsheet column type that identifies the source sample or compound from which aliquots/derivatives are created. |
Children Column | A Labsheet column type that lists the aliquots or derivatives created from a parent sample or compound. |
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Link Column | A Labsheet column that creates dynamic links to specific rows in a source Labsheet, enabling data integration via VLOOKUP-like functionality. |
Lookup Column | Read-only Labsheet columns that display data from associated columns of a linked source Labsheet, supporting Text and Number data types. |
Labspaces Magic Column | A read-only Labsheet column that lists names of Labspace pages (e.g., protocols, experiments) where a Labsheet row is embedded, with clickable links. |
Name of Protocol Magic Column | A read-only Labsheet column that lists names of protocol pages where a Labsheet row is embedded, with clickable links to open the pages. |
Name of Experiment Magic Column | A read-only Labsheet column that lists names of experiment pages where a Labsheet row is embedded, with clickable links to open the pages. |
Last Modified At Magic Column | A read-only Labsheet column that displays an up-to-date timestamp of when a Labsheet entry was last modified (e.g., updated values, assigned location). |
Existing Manifest Magic Column | A read-only Labsheet column that shows the name of the manifest (e.g., box or well plate) holding a Labsheet sample, with clickable links to open the manifest. |
Reference Column | A Labsheet column type that creates connections between different Labsheets (e.g., linking patient info to sample info), enabling data integration. |
Barcodes |
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Barcode Type | A setting in Labsheets for selecting the barcode format (1D or 2D) for printable labels used in sample tracking. |
Barcode Format | The file output type for printable barcodes in Labsheets, such as PDF, ZPL, or CSV, for compatibility with printers or external platforms like Brady Workstation. |
Print Labels | A Labsheet feature to generate printable barcode labels for samples or compounds, customizable with metadata fields and printer compatibility (e.g., Zebra, Brother). |
Scan Barcode | A Scispot feature to scan barcodes (via device camera or scanner) to access sample details and storage locations in Labsheets or Labspaces. |
Associate Barcode to Existing Item | A Scispot feature to link external barcodes to existing sample records in Labsheets, enabling integration without relabeling. |
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QC Automation Alerts |
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Alerts | Timely notifications in Labsheets for monitoring lab events like low inventory, reagent expiration, equipment maintenance, temperature, volume, or equipment availability. |
Alert Rules | Configurable conditions in Labsheets for triggering Alerts, based on parameters like quantity thresholds, expiration dates, or temperature limits. |
Alert Action | A task or response triggered by an alert in Labsheets, such as notifying users or prompting inventory reordering, trigger a QC Check, or even modify the state of Labsheet entry. |
Notification Center | A centralized hub in Scispot for managing and viewing all Alerts, accessible alongside Slack and email notifications. |
Labspaces: Run your experiments & document collaboratively. Supports multi-user editing
Experiments: Design your experiments by embedding various sections by doing a \ (backslash)
Protocols: Design your protocols by leveraging existing templates or design them from scratch
Documentation: Document your standard operating procedures
Folders: Containers to store groups of experiments, protocols, and documentation
Template Library: Design and document your most frequently used experiments and protocols steps, so you don't need to start from scratch
Official Term | Definition |
Template Library | Repository for storing reusable experiment, protocol, and manifest templates to standardize lab processes. |
Protocol Pages | Pages for documenting small lab tasks with multiple steps, ensuring consistent execution (e.g., PCR setup). |
Experiment Pages | Pages for larger tasks combining multiple protocols, integrating them into a single experimental process (e.g., cell culture). |
Documentation Pages | Non-executable pages for storing SOPs, best practices, and compliance information (e.g., safety guidelines). |
Inventory Automation | Feature to automate inventory updates from protocol pages, tracking consumed or generated materials in Labsheets. |
Folders | Containers within Labspaces to group experiments, protocols, and documentation by project or workflow. |
Start/End Date | A Labspace feature to set and display the timeline of a protocol or experiment, aiding project management. |
Tags | Keywords added to protocol pages in Labspace to enhance searchability and organization. |
Favoritize | A Labspace feature to mark protocols as favorites for quick reference and prioritization. |
Clone | A Labspace feature to duplicate protocols for reuse them for sharing/archiving. |
PDF Ready Document | A Labspace feature to create PDF versions of protocol pages for sharing and documentation. |
Reviewer Approval | A Labspace feature in Experiment and Protocol pages to mark completed tasks or results for supervisor review, ensuring compliance and accuracy. |
Page Signing | A Labspace feature for certifying the completion of a protocol or experiment, ensuring compliance and accuracy before finalizing and locking the page from further edit. Can either request a reviewer to sign off or self-approve. |
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Embeds |
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Section Embed | A Labspace feature to create movable content blocks for organizing page content. |
Headings Embed | A Labspace feature to style headings with different font sizes for page organization. |
Text Embed | A Labspace default option for writing paragraphs within the note editor. |
Bulleted List Embed | A Labspace feature to organize items or key points in a concise, bulleted format. |
Numbered List Embed | A Labspace feature for creating ordered sequences, steps, or instructions in a numbered list. |
Tasks List Embed | A Labspace feature to create interactive checklists for tracking tasks and to-dos. |
Code Block Embed | A Labspace feature to embed code snippets or scripts with syntax highlighting for readability. |
Quote Block Embed | A Labspace feature to highlight important information or insights in a quoted format. |
Image Embed | A Labspace feature to embed and resize images within pages, with metadata supported via Labsheets. |
File Embed | A Labspace feature to upload flat files from a local drive into pages. |
Page Embed | A Labspace feature to embed other Labspace pages within a page for cross-referencing. |
Sheet Embed | A Labspace feature to create ad hoc scientific tables with color-coding, cell merging, and formula support for calculations like volume or standard deviation. |
Chem Editor Embed | A Labspace feature to embed and visualize chemical structures within pages. |
Sequence Editor Embed | A Labspace feature to embed molecular biology or protein structures within pages. Can edit DNA/RNA/Oligo/Protein structures. |
Labsheet Embed | A Labspace feature to integrate structured scientific data tables from Labsheets into pages for managing datasets and experiments. |
Manifest Embed | A Labspace feature to embed sample plates or boxes from Manifests into pages for easy reference to sample arrangements. |
Protocol Embed | A Labspace feature to add protocols from the Template Library into pages, creating a copy to preserve the original template. |
NCBI Embed | A Labspace feature to embed 3D structures from NCBI by pasting a link into pages. |
Table Embed | A Labspace feature to embed structured tables for displaying data within pages. |
Sequence Embed | A Labspace feature to embed existing sequences from the library into pages. |
One Drive Embed | A Labspace feature to integrate and selectively embed files from One Drive into pages. |
Google Drive Embed | A Labspace feature to integrate and selectively embed files from Google Drive into pages. |
Location Manager: Track and manage the location of your samples and inventory.
Official Term | Definition |
Chain of Custody | A graphical timeline view in Labflows tracking a sample’s journey from collection to report generation, with audit logs for compliance. |
Activity Log | A detailed record in Labflows of every workflow step (e.g., order reception, testing, reporting) for transparency and traceability. |
QC Checks | Pre- and post-processing quality control checks in Labflows to ensure sample data integrity and test accuracy (e.g., checking barcodes, instrument calibration). |
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Flow | A workflow in Labflows for managing the sequence of steps in sample processing, from registration to testing and reporting, with options to assign samples to existing or new workflows. |
Orders | Requests for diagnostic tests or analyses, containing patient details, test requests, and associated samples, manageable in Labflows and Labsheets. |
Order Manager | A special Labsheet inside of Labflows to receive, register, and manage orders, capturing essential information like patient details, associated samples, test requests. |
Order Association | The ability in Labflows and Labsheets to link samples to orders at any workflow stage, enabling dynamic updates and unified processing. |
Patients Manager | A special Labsheet inside of Labflows to manage patient details (e.g., name, date of birth) associated with orders and samples in Labflows, ensuring accurate clinical data tracking. |
Sample Manager | A special Labsheet inside of Labflows for managing and tracking sample data, including accessioning, custom views, and Labflow assignments |
Sample Registration | The process in Labflows of logging and tracking samples (new or from storage) with unique identifiers, linking them to orders for traceability. |
Working Samples Creation | A Labflows feature to generate aliquots or derivative samples from registered parent samples for testing. |
Batch Samples | A group of working samples processed together in Labflows, each with a unique identifier for traceability across diagnostic tests. |
Test Management | A Labflows feature to select and assign diagnostic tests to samples, ensuring protocol compliance |
Report Generation | A Labflows feature to automatically create detailed reports with activity logs for approval and compliance. |
QC |
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Automated Data Flagging | A Labflows feature that automatically flags missing or incomplete identifiers and metadata (e.g., Sample ID, patient metadata) to ensure data integrity before workflow progression. |
Scheduled Maintenance and Calibration | A Labflows feature that automatically schedules equipment maintenance and calibration, sending alerts for upcoming tasks to ensure operational reliability. |
Expiry Tracking | A Labflows feature that tracks inventory item expiry dates and flags items nearing expiration, sending alerts for timely replenishment. |
Pre-Analytical Hold | A Labflows feature that halts workflow progression for samples with missing or incomplete pre-analytical data (e.g., barcodes, metadata) until resolved. |
Analytical Hold | A Labflows feature that flags and holds samples failing QC checks during analysis, requiring review before proceeding or rerunning. |
Post-Analytical Hold | A Labflows feature that prevents report generation for samples until all pre- and post-analytical QC issues are resolved, ensuring data accuracy. |
Pre-processing QC 1 | Initial quality control checks in Labflows to verify sample information (e.g., number of samples, barcode labels, physical state) before order registration. |
Pre-processing QC 2 | Secondary quality control checks in Labflows before testing, ensuring proper setup (e.g., inventory quantities, expiry dates, instrument calibration). |
Post-processing QC 1 | Quality control checks in Labflows after testing to validate results (e.g., standards within QC range, outlier detection via CV% or Std Dev). |
Post-processing QC 2 | Final manual quality control check in Labflows to verify the accuracy and completeness of test results before report generation. |
Term | Definition |
Root Location | A top-level storage area in Location Manager, such as a lab room or freezer, used to organize inventory. Retired location type. |
Child Location | Sub-level storage areas within a Root Location, such as shelves, drawers, or racks, for detailed organization. Retired location type. |
Node | Generic organizational units in Location Manager used as a catch-all for locations like rooms, freezers, or other areas before specific types were introduced. Retired locaiton type. |
Rooms | General-purpose physical spaces in Location Manager for organizing lab inventory, such as a lab room. Cannot be nested inside of any other location. |
Freezers | Storage areas in Location Manager with temperature display and tracking for sample preservation. Can be a standalone location, or sublocation inside a room. |
Shelves | Organizational units within rooms or freezers in Location Manager for arranging equipment or racks. Can be a standalone location, or sublocation inside a freezer or room. |
Rack | A storage structure within Location Manager for precise positioning of manifests, like boxes or well plates. Must be a sublocation of a room, freezer, or shelf. |
Manifest Previews | A Location Manager feature to view labels, tags, and samples in a manifest without navigating away, with hover details and single-click editing. |
Location Activity Log | A record in Location Manager tracking changes and actions specific to a location for visibility and traceability. |
Move Location | A Labsheet feature to assign samples or manifests to a specific storage location in Location Manager, either existing or new. |
Manifests: Design your multi-well plates, boxes, or other visual maps.
Official Term | Definition |
Well Plate | A type of manifest in Scispot for organizing samples in a grid format, typically with 96 or 384 wells, used for assays or storage. |
Box | A type of manifest in Scispot for storing samples in a box configuration, such as 10x10 or 9x9, used for inventory management. |
Checkout | A Labsheet feature to assign selected samples to a specific manifest, such as an assay plate or box, from the floating toolbar. |
Tags | Metadata keywords assigned to manifest wells in Scispot to categorize and enhance searchability of assay plates or boxes. |
Sample Label | A manifest label indicating a sample placed in an assay plate or box, used for tracking and identification. |
Positive Control | A manifest label for a control sample in an assay plate expected to produce a positive result, ensuring assay validity. |
Negative Control | A manifest label for a control sample in an assay plate expected to produce a negative result, ensuring assay accuracy. |
Standard | A manifest label for a reference sample with known properties in an assay plate, used for calibration or comparison. |
Blank | A manifest label for an empty or non-reactive sample in an assay plate, used to establish a baseline for measurements. |
AI Analytics: Slice and dice your Labsheets data using GUI (Graphical User Interface) and SQL.
Term | Definition |
AI-Powered Dashboards | Scispot feature for real-time visualization and interaction with R&D, production, and operational data, customizable via widgets on the homepage or Labsheets. |
AI Widget | Customizable visualization component in Scispot’s dashboards, such as AI Charts or AI Metrics, generated from Labsheet data for insights like KPIs or trends. |
AI Chart | A type of AI Widget in Scispot for creating data visualizations (e.g., graphs) from Labsheet data based on user prompts. |
AI Metric | A type of AI Widget in Scispot for displaying performance indicators from Labsheet data based on user prompts. |
Custom Prompt | A user-defined instruction in Scispot’s AI-Powered Dashboards or AI Assist to specify the data or metrics to analyze and visualize from Labsheets. |
Generate Chart | A Scispot dashboard feature to create a visual chart (e.g., AI Chart) based on a user prompt and selected Labsheet data. |
Python Code Tab | A Scispot dashboard feature to view the AI-generated Python code used to create custom charts or metrics in AI dashboard |
Refresh Button | A Scispot dashboard feature to manually sync and fetch the latest Labsheet data for AI Widget generation. |
Edit Widget | A Scispot dashboard feature to modify an existing AI Widget by changing the prompt or regenerating the chart or metric. |
AI Card | A pre-generated or custom visualization component in Labsheet-specific dashboards, created via AI Assist or user prompts to display data insights. |
Initialize Dashboard | A Scispot feature to activate a Labsheet-specific dashboard, generating out-of-the-box AI-powered cards for data visualization. |
Add Card | A Scispot dashboard feature to create a new AI Card in a Labsheet-specific dashboard by specifying a prompt for data visualization. |
App Store: Integrate Scispot with 3rd-party apps and enable native app extensions.
Jupyter Hub: Connect Jupyter Notebook with Scispot to access and analyze lab data stored across Scispot apps.