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 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!
Scilligence Achieves ISO 27001 Certification: A Milestone in Information Security
January 29th, 2024
Scilligence Corporation, the leading provider of a unified informatics platform for small molecules and biologics, has attained ISO 27001 certification, marking a significant milestone in our commitment to information security. Certification was achieved after the successful completion of an 8-month audit.
ISO 27001 is the accepted global benchmark for demonstrating your information security management system (ISMS). This accreditation ensures that we comply with the best practices in information technology and demonstrates our ongoing efforts toward maintaining information security.
At Scilligence, we understand the paramount importance of data security in today's digital landscape. Our commitment to obtaining and maintaining ISO 27001 certification reflects our unwavering dedication to prioritizing the confidentiality, integrity, and availability of our customers' data.
About Scilligence
We provide a versatile and tailored scientific informatics platform designed to foster collaboration, boost productivity, facilitate data-driven decision-making, and ensure robust compliance and data security. Through the utilization of our integrated toolset, organizations can optimize their R&D workflows, expedite innovation, and propel scientific discoveries forward.
Scilligence offers a suite of premium products to cater to your specific requirements:
Scilligence ELN: A Cross-Platform Electronic Lab Notebook for Chemistry and Biology
Scilligence RegMol: A Cross-Platform Registration & Assay Database for Biologics, Small Molecules, and Conjugates such as ADCs
Scilligence Inventory: A Cross-Platform Inventory System for Life Science R&D
Scilligence PMF: A Project, Workflow, and Customer-Relationship Management System for Life Science R&D
Scilligence SDMS: A Cross-Platform Scientific Data Management System
TouchMol4Office: A tool that empowers Cheminformatics and Bioinformatics within Microsoft Office, seamlessly integrating informatics into your daily operations
ELN for Academic Research: A Success Story
September 11, 2023
The Problems with Paper Notebooks
“Hey, I think someone ran that reaction a few years ago, why don’t you go check in their notebook?”
Have you heard this request from your PI and immediately thought…
Yeah. I’ve been there.
I remember thinking even if I managed to find the right page, I would have to undertake a second and equally arduous journey to find the associated NMR spectra and other characterization data.
Safe to say that in the digital age… Data is King
The ability to digitally store, share, mine, and process data is the foundation of how we work today. So why as chemists and biologists in academia are we continuing to confine our most valuable data, our experimental records, to paper notebooks on neglected shelves, the same way scientists have done since the 19th century?
In the age of database searches, word processing, file sharing, and email surely there must be a way to digitize the scientific process?
These were the questions being asked in Prof. Shih-Yuan Liu’s Research Group at Boston College in 2015 when we decided to start the search for an electronic lab notebook (ELN).
The ELN Solution: Digital Notebook, Searchable Database
Aside from a searchable data repository for all our reactions, there were other features motivating us to make the jump from paper to digital. We were looking for a way to standardize lab notebook entries to improve record keeping and a platform that would encourage collaboration and information sharing.
Most organic chemists are familiar with the software ChemDraw®, the chemical sketcher tool; we knew that having a similar sketcher in a digital notebook entry would save a lot of time over hand-drawing reaction schemes. Organic chemists often run the same or similar reactions multiple times, therefore having the ability to copy or refer to experiments would be very useful.
In a paper notebook, the lack of a copy-paste feature fosters some poor record-keeping habits, such as certain lab member’s tendency to just write “see page XX” instead of filling in crucial reaction details for a repeated reaction.
While the benefits of features like copy-paste seemed pretty straight-forward, we did not have a sense of the life-changing improvements adopting an ELN would bring prior to starting our evaluations.
Here are the three important lessons I learned about finding ELN that is right for my lab:
1) Use the ELN as if it were already your notebook! While it takes more effort, the only way to put an ELN through its paces is to record real experiments with real data. A few days of using an ELN provided a good picture of how it would fare over the next few years.
2) No ELN is perfect! Just like with any software, there will be some quirks and features that not all users will like. Decide as a group what aspects of the software are simply inconvenient and which ones are deal breakers.
3) Change is difficult! Adopting a new piece of software or learning how to use any new tool can be a challenging process. Be patient, stick with it, and form a consensus on how the new software will be implemented.
Following our review process, the Scilligence ELN became our ELN of choice with its combination of an excellent search feature, convenience, time saving tools such as copy experiments, reagent lookup, direct integration with NMR, robust performance, and competitive price point.
The Scilligence team worked closely with us to deploy their web-based software, trained us on how to use it, and applied a few customizations.
A few months after we started our search for an ELN, we bid farewell to paper notebooks!
Experiencing the benefits of adopting the Scilligence ELN right off the bat!
Several features of the Single Step Reaction form, an ideal template for synthetic organic chemistry experiments, significantly reduced data entry time. The reaction scheme editor populates reagents from a database search, simultaneously pulling in key information like MW and MF. The stoichiometry table automatically calculates amounts and ratios. After the software does most of the heavy lifting by filling in the reaction scheme data, generating a procedure is even more straightforward.
With the recipe feature, a scientist can generate a generalized experiment template and share it with the whole group; the recipe pulls in reagent information, leaving only a few minor adjustments to be made.
In addition to saving time for individual notebook entries, the ELN makes information sharing much more efficient. Our group used the project documents as a central location for sharing references, SOP’s, presentations and other group project materials. Before the ELN, we had to recreate all our paper reaction schemes in ChemDraw® and then paste them into PowerPoint slides for group meetings. Using the ELN allowed us to start holding group meetings and presentations right in the ELN environment, with researchers projecting their notebook pages on a presentation screen.
Professor Liu could now monitor the entire groups’ notebooks from the comfort of his own desk!
I experienced the greatest impact of using the Scilligence ELN when it came time to write my thesis.
Instead of having to dig through instrument computers to track down data, process that raw analytical data into spectra, and chase down that one reaction with the highest yield, all my data was already present in a centralized, fully searchable database.
I defended my PhD thesis at Boston College in May 2019 and went on to work in materials research at a government contractor. This year I returned to Scilligence as an employee, working as an Application Scientist in Presales Support. The Boston College Chemistry Department continues to use Scilligence ELN and to build an ever-expanding database that will be far more valuable to researchers than forgotten notebooks on dusty shelves!
Scilligence is working on an ELN catered to academic institutions so that more student researchers can access the tremendous benefits of a digital scientific workflow. This ELN will streamline the lab notebook experience and encourage collaboration by providing a digitized and paperless way to work on experiments and projects at every step. Browse experiments across multiple notebooks, harmonize the format of data content, quickly search for specific information, and prevent the loss of existing laboratory knowledge when researchers leave.
Scilligence 6.8 Release Notes
April 16, 2021
ELN 6.8.0 Release Notes
User Functionalities
Error Reporting
ELN Forms
Dose Response Curve
Security
Display
General Fixes
Inventory 6.8.0 Release Notes
Compound Management Improvements
Cart Improvements
Containers Improvements
Customization Capabilities
Language Improvements
Admin Capability Improvements
Compound Requisition improvements
RegMol 6.8.0 Release Notes
Registration Improvements
Explorer Improvements
Assay View and Assay Improvements
HELM to Structure Optimization
RegMol and Inventory Integration
Admin and Security Features Improvement
Scilligence 6.7 Release Notes
ELN v6.7.0 Release Notes
Hybrid Free Form – only actual data can be pushed to RegMol.
Improved Registration and Inventory integration
Improved Study Report
Updated Protein Purification template
Improve Curve Assay template
Improve security integration, including OKTA and Azure
New file previewer
Improved HELM features
JSDraw supports Pictures
Able to set colors to individual HELM monomers
6.7.0 Inventory Release Notes
Improved compound management workflow
Improved searching
CAS integration
Improved compound requisition workflow
Improved bulk importing
6.7.0Release Notes for RegMol
Improved bulk registration
Improved admin tools on data curation
Improved chirality check
Support parent/batch synonyms
Improved HELM registration
Clean up for HELM-atom/bond hybrid structures
PMF
Improved workflow engine
Improved document management
New file previewer
SDMS
New file previewer
Improved RESTful APIs
Scilligence 6.6 Release Notes
Scilligence ELN 6.6.0
Shared Notebooks - Users can share notebooks like co-authored experiments - Owner can rename a shared notebook - Improved Formulation Templates
Improved HELM functionality - Support HELM repeating units - Able to expand HELM nodes - Improved HELM monomer replacement
Summary of plate experiments details - Thumbnail for plate map - Display number of assay plates and compounds - Display submitted assay results
Improved audit trail - Changes to experiment and notebook names tracked - All witnesses included in experiment export
Fixed MF/MW calculations - Small Library form automatically calculates - MF updates correctly when structure changes and salt remains
User functionalities - Ability to batch export user information - No refresh needed when adding users, appear automatically in UI - Improved re-fitting of QC Curve data in the Dose Response Form
Scilligence Inventory 6.6.0
CAS Integration and Improvements - Name to structure using CAS - Automatic CAS and structure generation - Up to date CAS Registration numbers - Search structures via with CAS
Bulk Import - Automatic CAS lookup during bulk import - User experience improvements - Ability to create new locations during bulk import
New Role – Purchase Stockroom - Restricted role that can import product/lots/contains and change container location - Role cannot modify in stock products
Access control - New customization functions such as restriction based on site and department
Scilligence Focus 6.6.0 - Ability to Synchronize RegMol Assays and Projects - Ability to Upload Data Using Files - Improved Filtering - Improved Sorting for Multiple Fields - Improved SAR Analysis - Improved Charting - Ability to Download Data
Scilligence 6.5 Release Notes
ELN 6.5
Shared notebook feature allows project members to create experiments and collaborate in a single notebook.
RegMol 6.5
Improved API Key management allows customers to use RESTful APIs more easily and securely.
Batch Explorer UI has been improved with pagination and more options for sorting and filtering data.
Cart feature has access to many more data fields and enable better configuration/customization of data table for exportation into SDF, Excel, or csv.
Inventory 6.5
Bulk import or update location function allows users to easily configure their location tree by importing an Excel file as well as make changes to existing location trees.
Improved access control logic and documentation for management and customization of user roles.
New plate history tracking allows users to record an audit trail for assay plate
Improved compound management with plate scanner allows users to automatically create changes and calculations within a plate.
Users now have the ability to change a location and sub-location so that containers can no longer be added to full locations.
PMF 6.5
Improved Gantt chart for managing tasks and actions
Multiple users can now edit large documents simultaneously with new Collaborate Editing Document (CED) feature
Copy and download options added to projects and tasks for more flexibility
All Modules
Updated JavaScript PDF viewer allows more flexibility for previewing experiments and documents
Improved API Key management allows customers to use RESTful APIs more easily and securely.
RegMol 6.1.0 Release
Scilligence RegMol is a web-based registration database and assay data repository for biologics, small molecules, and conjugates. Some of RegMol’s many offerings include a powerful structure and bio-sequence search, batch registration, assay protocol management, and data mining analytics. RegMol’s comprehensive and easy-to-deploy platform empowers centralized data management and collaborations for life science research and development.
RegMol 6.1.0 includes the following improvements and changes:
Improved HELM Registration
New Assay Raw File and Plate Management
Improved Curve Fitting
New Assay Pivot function using Assay View
Revamped Admin menu
Bug Fixes
ELN 6.1.0 Release
Scilligence ELN (Electronic Laboratory Notebook) is a powerful platform for facilitating internal R&D and managing external collaborations. It comes with advanced informatics for biologics and small molecules, thus also supports conjugates such as antibody-drug conjugates (ADCs). Our ELN supports all disciplines of research including medicinal chemistry, process chemistry, bioassays, HTS, in vivo pharmacology, and toxicology. Widely adopted by industry and academic institutions, Scilligence ELN is easy to use, integrate, and deploy across all platforms.
Scilligence ELN 6.1.0 includes the following changes and improvements:
Improved Co-Author function
Improved Multi-factor Authentication (MFA)
Improved Flex-Form
Improved Form Manager
Improved Invention Management
Improved Final Report Module
ELN-in-Office integration
Revamped Admin menu
Bug fixes
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