Author: Scilligence

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Inventory 7.0 Release Notes

Location

Products, Lots, Containers

  • CAS No can provide Chemical Lab Safety information of specified compound from SafeScience (Upon Request)
  • Improved metadata log surrounding deleted containers
  • Low Stock Quantity alert includes sum of all container quantity indicated at Container level (Upon Request)
  • Admin can define label and associated prefix for Container Types 
  • Improved search bar autosuggest function for custom columns (Upon Request)
  • New Inventory category: Plasmid
  • Create multiple containers at one time
  • Allow and track multiple transactions of Submitted Amounts, Test Type, and Purpose using ‘Partially Use’ table  (Upon Request)
  • Improved sort and filter for Products, Lots, and Container tables
  • Consolidated Container functions into respective categories: Export, Print, Options, Edit Location
  • Improvements to ‘Pack’ function

Formulation

▪ Improved packaging functionality

Compound Management

  • Count capabilities for Compound Management queries (Upon Request)
  • Ability to search containers in Compound List query using Project Code
  • Implemented sort and filter functionality in Containers table
  • Improved Bulk-split function

Actions and Barcode Operations 

  • ‘Partially Use’ barcode operations ‘Amount’ field do not require ‘qty’ unit after value – set by default
  • Display plate barcode metadata when performing solvation barcode operation (Upon Request)
  • Compound ‘Status’ can be modified while use ‘Change Owner’ command (Upon Request)
  • Plate Solvation command now pulls value from plate dialog window into container level column fields (Upon Request)

UI/UX

  • Added Dark Mode function
  • Harmonized cart icons across apps
  • Cart page can now filter and sort columns directly
  • Custom columns can be displayed in Cart and exported as CSV (Upon Request)
  • Revamped colors, icons, logo, and layout for Inventory
  • AccountIDs of users are displayed for Admin and SysAdmin roles
  • Ability to bulk-import projects and users using .xlsx, .csv, or UI table with Read/Write/Manage access
  • Projects can now be filtered
  • Improved ribbon menu set on left panel
  • Improved icon for users when changing parent of lots
  • Project Code and Project Name support wildcard search
  • Inventory form background color match application background color in light mode
  • Companies and associated contacts can be deleted in bulk at the parent level
  • Entire list of Companies now populates when selecting root-level category
  • Users now receive warning of existing daughter-level components when deleting parent-level fields
  • Ability to print barcode from Bulk-Update and Bulk-Import pages
  • Importing Tare weight display number of successful and failed imports 
  • Statistical reports can populate data from custom columns (Upon Request)
  • Fixed login issue with ‘Reset Password’ redirection
  • A warning now populates when the total amount of new container is greater than the total sum of containers being merged

API and Integration

  • Updated Inventory Swagger page documentation API 
  • Added API for Locations
  • Updated webservice integration
  • Comments can be added to selected node after modification
  • General improvements to RegMol-Inventory integration

RegMol 7.0 Release Notes

UI/UX

Administration and Installation

  • Ability to manually force creation of a new parent (ignore uniqueness check)
  • All batch data of a parent can now be edited simultaneously through an Admin tool
  • Allow entity association to multiple projects
  • Bulk Import tool now marks job for potential deletion
  • Chemistry role now has access to limited batch information
  • Email notifications are now only sent to active project managers
  • Resolved issue where Parent Explorer was not visible without proper role
  • Viewing all entities can be turned off based on project membership
  • When a project manager creates a project, they are automatically added as manager of that project

Assay Protocols and Views

  • Better error handling for Select-type assay protocol column
  • Can now download images in assay columns to Excel
  • Can now save column mappings for Assay Views uploads
  • Charts in Assay Views are better rendered
  • Improved Assay Results filtering with value comparators "><≤≥±"
  • Improvements to Assay Results page
  • Improvements to single-column pivoted Project Portal view
  • Unused fields in batch-level Assay Results view can now be hidden

Significant improvements to Assay Views

  • Easier selection of structure batch/parent properties
  • Column sorting and filtering
  • Drag to change column order in a table
  • In-table aggregation
  • Support for large datasets in web browser
  • Color coding

Cross-application Integration

  • Added functionality to allow for container fields to show in Project view Molecules tab
  • Bulk Upload tool can now be used for 'Push to Inventory'
  • Can now accept json input for API registration
  • Can now add file to batch by API
  • Can now add files to Assay Results via API
  • Can now push Parent Name, Polymorph, Alias, Pre-Registration ID, etc. to Inventory
  • Can now sync Project to Inventory
  • Now able to hyperlink to pre-registration notebook via customization
  • RegMol-side support for filling compound plates from raw spreadsheet data in ELN

HELM

  • Additional characters are available for use in HELM monomer symbols
  • More descriptive error message when trying to edit a monomer already used in structures

Performance

  • Code Optimization and Performance Tuning

Registration Improvements

  • Ability to show all structures regardless of stereochemistry in Choose Parent dialog box
  • Added ability to include parent level attachments
  • Added ‘Edit Comments’ button in Pre-Registration List table
  • Allows underscore option within registration ID as delimiter in addition to dash
  • Bulk Import tool can now accept any type of entity via dropdown
  • Can now download directly from Entity Lists
  • Can now handle pure-digit parent IDs
  • Harmonized nomenclature: Entity for Molecule and Compound
  • Harmonized export of Parent Description column header
  • Improved authentication for desktop Bulk Import tool
  • Improved entity specific uniqueness check
  • Improved handling when trying to register an entity drawn in JSDraw with structure error(s)
  • Improved logic for virtual entity relationships
  • Improved logic to parent alias columns
  • Improved uniqueness check for mixtures
  • Improvements to Bulk Update
  • Improvements to handling of Bulk Registration sessions
  • Modified Date field added to Batch/Parent explorer
  • Optional additional constraints for batch and parent editing
  • Pre-registration notification email now has a URL link
  • Significantly improved entity history to now show edit changes
  • Updates to controlled vocabulary on "Admin >> Data Management >> Assign Entities to Projects" page now allows for multiselect fields

Salt Handling

  • Added a check to make sure formal charge does not change during neutralization
  • Added neutralization and salt stripping to "Check Parent" and "Check for Duplicates" functionalities on Bulk-Register page
  • Bulk-Register now able to handle mixed salt names and salt codes.
  • Enabled fractional salt stripping capabilities
  • Key added to remove automatic capitalization

Search and Explorer

  • Able to do structure search to find component structures for Mixture and Formulations
  • Added ability to list custom columns in Batch Explorer table using key
  • Download All/Selected as CSV/SDF, button added to Advanced Search Results tab
  • Harmonized order of data fields in Batch Explorer
  • Improved search results when exact match found
  • Improved sequence search allows for exact or partial matches in Batch Explorer

ELN 7.0 Release Notes

General

Single-Step Reaction Template

  • Optimized calculations for the SSR when ratios are involved
  • Preserve data in the 'Request Details' table when using the 'Create Next Step' feature so that it is consistent in the new experiment
  • Enable option to set default units for concentration form field in reactants table (in the SSR)
  • Decimal point definition (2 places) for unit amounts and volumes in the SSR
  • Yield values can be rounded to integer values (no decimal points)
  • Expand display for decimal points for values entered in tables in the SSR form (in addition to scientific notation)
  • The number of characters used to represent Reagents can be limited (to truncate the names)
  • Optimized rendering of Reaction Path for multi-step reactions
  • General bug fixes

Flex Form

  • Users can now automatically locate newly created components within the Experiment
  • Dialog box is displayed if the Configuration IDs are missing from the FormXML to remind the User to add this information
  • Added additional fields in the Flex Form for increased User customization
  • General bug fixes

Assay Data Templates

  • Optimized calculations for plate templates
  • Enhancements to how data readers parse compound IDs from raw data files
  • Added capability to upload assay results to multiple protocols at the same time
  • Improvements to data reader script command parsing
  • Users can now exclude data points (from raw data tables) when generating curves
  • Read multiple readouts and simultaneously calculate delta values
  • Default values can be specified for data reader READ function
  • General bug fixes

PDF Rendering

  • Improved PDF rendering of Experiments. This is especially helpful for SSR forms where multiple columns are exported as part of the PDF
  • Enable export of template FormID to the footer of a PDF
  • Set defaults to font regulations (type, size, and spacing) that must be observed in documents submitted to the FDA when rendering PDFs
  • Co-Author information is now included in exported PDFs
  • Custom logos (images) can be added/removed from exported PDFs
  • Borders for tables can be removed when exporting PDFs
  • Allow for centering of form field contents
  • SDMS files are exported as Attachments when rendering Experiments as PDF
  • Columns for checkboxes are not included in PDF exports (minimizing the space taken)
  • Standardized how headers and footers are rendered in PDF export along with font displays
  • General bug fixes

Security and Access

Witnessing

  • Admins can now re-assign Witnessing tasks to other Users. This is helpful if the original Reviewer is not available
  • Optimized the Closing and Witnessing workflow for Experiments
  • Added option for adding second Reviewer using a linear witnessing workflow
  • External Users can view Experiments sent to them for witnessing if they have the appropriate access rights
  • Expanded roles that can re-open a Closed Experiment (default configuration is limited to Admins)
    • Addition of additional reviewer when closing Experiments
    • Removed limitation where only Admins were able to review Experiments
    • Added field for Reviewer to enter their notes when rejecting an Experiment review request

Co-Author

  • Co-Authors will need appropriate access (same as Authors) to view Experiments and Attachments
  • Email notifications can be configured to be sent when a Co-Author is created
  • Co-Authors can now see other Users that are editing the Experiment

Admin Permissions

  • Admins can now set retired ELN templates as non-User Creatable to prevent templates from being copied
  • Admins can limit the number of open Experiments in a Notebook while prompting open Experiments to be closed
  • Enabled option to limit PDF export of Experiments to Admin Users only
  • Admins can be assigned only SysAdmin accounts
  • Enabled Admins to open or close multiple Projects at one time
  • Added Project-specific information for Admins when searching for Users
  • Expanded framework for Admin access to enable different types of Admins This will help fine-tune access based on client needs

Project Manager Permissions

  • Project Managers are now able to import Projects
  • Project Managers and Admins can now edit and save SOPs/Templates

Internal/External Permissions

  • Display of reactant, reagents, and products in the JSDraw editor can be limited to internal Users
  • Automatic sorting of internal vs external users in ELN

SSO

  • Added support for SAML SSO
  • Disabled local login for Users signing with SSO solutions

Audit Trail

  • The Audit Trail of an Experiment now captures information on order changes made to attachments, when components of a reaction are modified in the SSR template, and when publications are edited
  • Enhanced tracking of all export actions of the Experiment and Attachments

Other

  • Locally encrypted files can be decrypted in the ELN (after uploading to the ELN). This requires the use of a decryption interface
  • Added support for third-party encryption and decryption software to decrypt the files uploaded to ELN and encrypt the same when they are downloaded locally
  • Enabled sharing of Templates/SOP across Sites and Departments
  • General bug fixes

UI/UX

User Interface Improvements

  • Revamped colors, icons, and layout for the ELN app
  • ELN form templates can be further nested in menus allowing for better organization
    • UI notifications are visible as bubbles for Team Discussion
    • Minor updates on how information is displayed for the Cart, User, and Password Change screens
    • Newly created Notebooks and Experiments are displayed on top (descending order) by default in the Main List
    • Added additional fields to Project Compounds tab (to mirror what is present for the Compounds)
    • Optimized how columns are hidden in Experiments
    • The width of text editor windows can be set to different sizes for better screen display and PDF rendering
    • Added a space (non-printing character) in the form field for amount between units and numbers
    • Optimized email reminder notifications for Experiments to be closed and Experiments sent for review
    • Increase the size of the dialog window that is displayed when reviewing Experiments
    • Headers of tables in Experiments can be set to wrap (to display in 2 lines)
    • Display Voided and Closed Notebook in My Notebooks section of the Homepage

User Function Improvements

  • Added additional fields when importing bulk-importing Projects to minimize User input
  • Optimized bulk importing Users to the ELN
  • Enhancements to URLs display for Experiments for sharing
  • Enabled batch-editing of Instruments in the ELN
  • Search using Table Headers, contents within tables, and Folder name, is now possible
  • Users will automatically jump to the next approval task as they go through the list when there are multiple approval tasks in the Task list
  • Optimization of preview of PDF files within the ELN app
  • ELN templates can now be saved/favorited for quick access
  • Project Codes can now include both uppercase and lowercase characters (default display was uppercase characters)
  • Added filtering options for Users by Department
  • Add filter for Project Code in the Main List for filtering purposes
  • Custom categories can be automatically added to the drop-down menu of category filters eliminating the need for the user to manually enter filter(s)

Attachments

  • Enabled edit buttons for Attachments when using the ELN4Office add-on in the ELN
  • Prevent auto-collapsing of Attachments section if the User expands the same section and refreshed the Experiment page
  • Attachments can also be downloaded with a dedicated button from form fields where they are uploaded
  • Enabled batch downloading of Experiment Attachments

Final Report Feature

  • Updated headers for columns for the Final Report feature
  • The Final Report button will not appear if the add-on is not enabled

 

Material/Instruments/Reagents Tables

  • Enhanced filtering for Materials in the ELN
  • Materials with duplicate names can be used
  • Instruments, Reagents, and Materials page is filterable and sortable

Character Rendering

  • Improved support for Chinese characters throughout the app
  • Added support for Korean Hangul characters

Timestamps

  • Optimized display of timestamps for Projects when servers are in different geographies (from where the User is accessing the ELN)
  • Timestamps entered in text box (as tokens) are synced to server where the ELN app is hosted

Audit Trail and Witnessing

  • The status of an Experiment is automatically updated after the Reviewer approves an Experiment
  • Added additional details in the Audit Trail when Users make changes to Experiments

Explore: Projects, Notebooks, and Experiments

  • Enhanced pagination options when displaying list of Projects, Notebooks, and Experiments
  • Enhanced export options for Projects, Notebooks, and Experiments (in bulk)

Other

  • Advanced reporting in the ELN for error messages
  • General bug fixes

Scilligence 6.6 Release Notes

Scilligence ELN 6.6.0

  1. Shared Notebooks
    1. Users can share notebooks like co-authored experiments
    2. Owner can rename a shared notebook
  2. Improved Formulation Templates
  3. Improved HELM functionality
    1. Support HELM repeating units
    2. Able to expand HELM nodes
    3. Improved HELM monomer replacement
  4. Summary of plate experiments details
    1. Thumbnail for plate map
    2. Display number of assay plates and compounds
    3. Display submitted assay results
  5. Improved audit trail
    1. Changes to experiment and notebook names tracked
    2. All witnesses included in experiment export
  6. Fixed MF/MW calculations
    1. Small Library form automatically calculates
    2. MF updates correctly when structure changes and salt remains
  7. User functionalities
    1. Ability to batch export user information
    2. No refresh needed when add users, appear automatically in UI
  8. Improved re-fitting of QC Curve data in the Dose Response Form

Scilligence Inventory 6.6.0

  1. CAS Integration and Improvements
    1. Name to structure using CAS
    2. Automatic CAS and structure generation
    3. Up to date CAS Registration numbers
    4. Search structures via with CAS
  2. Bulk Import
    1. Automatic CAS lookup during bulk import
    2. User experience improvements
    3. Ability to create new locations during bulk import
  3. New Role – Purchase Stockroom
    1. Restricted role that can import product/lots/contains and change container location
    2. Role cannot modify in stock products
  4. Access control
    1. New customization functions such as restriction based on site and department
  5. Compound management
    1. Increased search control
    2. Improved search display

Scilligence PMF 6.6.0

  1. Improved CED Editing
  2. Improved Gantt Charts
  3. Improved Project Member Management

Scilligence Focus 6.6.0

  1. Ability to Synchronize RegMol Assays and Projects
  2. Ability to Upload Data Using Files
  3. Improved Filtering
  4. Improved Sorting for Multiple Fields
  5. Improved SAR Analysis
  6. Improved Charting
  7. Ability to Download Data

ELN4EDU-details

Bring an industry-essential asset to your research group

ELN4edu is a platform for recording experiments, building a searchable database, and collaborating on research projects, all supported by our proprietary cheminformatics tools: JSDraw Sketcher and Chrawler Search Engine.

With ELN4edu, bring the benefits of an industry-essential asset to your research group.

Benefits

  • Centralized, searchable database
  • Built-in cheminformatics
  • Upload any data type
  • Establish templates and SOP’s to standardize workflows
  • Build archives to benefit future researchers
  • Improve efficiency in the lab
  • Quickly generate presentations, reports, and publications
  • Collaborate, view data in real-time, and generate feedback

Capture the entire research process in one place

ELN4edu is an ELN tailor-made for academic researchers, ideally suited for smaller, chemistry-focused groups.

Tired of digging through paper notebooks to find that one reaction?

Can’t keep track of all those analytical spectra?

ELN4edu provides an affordable solution to the data silo problem.

Key Features

  • Chemistry reaction templates with built in structure and reaction sketcher
  • Stoichiometry tables
  • Create, upload, share templates and SOP’s
  • Create projects, project documents, manage users and projects
  • Reaction and structure search
  • View Office, PDF, and image files in-line
  • Copy experiments
  • Attach any data or file type
  • Export or print experiments for reports and publications
  • Sign, witness, and close experiments

Would you like a free trial?

Click the link below and fill out the registration form to set up your free trial account.

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LN4edu

The ability to store, share, mine, and process data is the foundation of work in the digital age; so why should scientists have to keep writing their experiments in paper notebooks?

Introducing ELN4edu, a digital workspace for academic researchers to record, process, and share their data.

Increase laboratory efficiency and reduce time to publication with ELN4edu.

Scilligence Insights: Evolving our Software

February 8th, 2024

At Scilligence, we have spent the last year exploring various avenues to enhance our scientific software. Using a three-pronged approach, we are committed to providing the tools necessary to optimize R&D workflows:

Partnerships for Expansion and Integration:

  • Currently partnered with CAS, Certara 360, Chemical.ai, Tetrascience, and Zifo.
  • Partnerships facilitate product expansion and integration by aligning business needs and workflows.

Features Development and Modality Enhancement:

  • Constantly developing new features and improving existing ones based on user feedback.
  • Unique capability to handle diverse modalities: small molecules, biologics, antibody drug conjugates, PROTACs, lipid nanoparticles, etc.
  • Focus on improving capabilities and workflows for each modality.

Customer-Centric Focus and Researcher Workflow Improvements:

  • Our strengths lie in a customer-centric approach, adapting and customizing to unique workflows.
  • Emphasis on quality of life improvements to make daily software use a pleasurable and productive experience.
  • Improvements to our roadmap process.

Key Features and Future Plans:

Version 7 Upgrade (October 2022):

  • New look and enhanced UI/UX.
  • Focused on functionalities for core products: Scilligence ELN, RegMol, and Inventory.

Version 7.2 (January 2024):

  • Further UIUX enhancements : improvements to existing modalities, templates and privileges to enhance end-user experience.
  • Streamlining of dataflow between Registration and Inventory Modules

Version 7.3 (Mid-2024) and beyond:

  • Introduction of a complete lipid nanoparticle (LNP) workflow across Scilligence ELN, RegMol, and Inventory including LNP design in ELN and RegMol, registration, capturing assay data, capturing containers, and tracking stability
  • Introduction of a formulations workflow across apps 
  • Conjugation form improvements in ELN. Includes conjugate builder function to build conjugates with registered entities, relationship registration, , and simplified customization process
  • Improvements in data capture flexibility using Microsoft Office in-place editing and reusable Flex forms.
  • Introduction of new biologically focused capabilities to ELN, including sequence display and manipulation, blast search, and sequence alignment.
  • Removal of XML layer for improved performance

As we embark on this journey of continuous improvement, Scilligence remains dedicated to providing solutions that streamline R&D processes, and drive innovation. 

Stay tuned for more updates!

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Intuitive Data Analysis

FOCUS allows users to analyze complex sets of chemistry and biology data interactively, identify lead molecules, visualize gaps in Structure-Activity Relationships (SAR), and accelerate drug discovery.

Data import and Charting

Within FOCUS, users can effortlessly import data from files, expanding the range of data sources you can utilize. Visualize chemical and biological data with chemically-aware charting and graphing tools, gaining a deeper understanding of your research.

Collaboration and Security

Collaborate securely in real-time, share findings, and maintain data integrity with robust security and compliance features. FOCUS ensures data privacy and regulatory compliance, while its adaptable framework allows for quick identification of lead molecules, gaps in SAR, and pathways for accelerating drug discovery and research.

 Seamless Data Integration

FOCUS is fully integrated with the rest of the Scilligence suite, allowing users to centralize chemical structures, biological assays, and experimental results from various sources, enabling easy access and unified analysis. FOCUS effortlessly brings together diverse data types, simplifying data management and facilitating cross-functional collaboration among research teams.

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Focus

Elevate your research with the Scilligence FOCUS module, which provides an intuitive and interactive solution for streamlined chemical and biological data analysis. The FOCUS module utilizes an adaptable framework that helps for quick identification of lead molecules. This allows FOCUS to help accelerate drug discovery by helping research teams to collaborate efficiently and make informed decisions.

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Project life cycle management

PMF is the central planning and control function for project management, defining how a project should be planned, implemented, monitored and closed.

Build and design custom workflows

PMF is an intelligent workflow design engine that provides you with a customizable solution for creating, managing and tracking your company’s business processes.

Make project plan online and track project progress

Project task templates streamline every aspect of planning and executing projects, while changes to the project plan can be controlled and approved by multiple users at any time.

Build enterprise internal knowledge base

Powerful indexing tool to search documents, emails, and notes.