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

New Office in San Francisco

Scilligence is pleased to announce the grand opening of its San Francisco office on February 17th, 2020! Our new location is 395 Oyster Point Blvd, Suite 209, San Francisco. We look forward to better serving our clients in the West Coast.

Our colleagues will be at Bio-IT West/Tri-Con (Booth #824) from March 1-4. Stop by and ask about our integrated solutions for life science R&D or about our open positions in California! Reach out to Scilligence at [email protected] to request a discounted session pass or a FREE pass for networking events and the plenary keynotes (including speaker Eric Topol).

Scilligence 6.5 Release Notes

ELN 6.5

  1. Shared notebook feature allows project members to create experiments and collaborate in a single notebook.

RegMol 6.5

  1. Improved API Key management allows customers to use RESTful APIs more easily and securely.
  2. Batch Explorer UI has been improved with pagination and more options for sorting and filtering data.
  3. 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

  1. 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.
  2. Improved access control logic and documentation for management and customization of user roles.
  3. New plate history tracking allows users to record an audit trail for assay plate
  4. Improved compound management with plate scanner allows users to automatically create changes and calculations within a plate.
  5. 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

  1. Improved Gantt chart for managing tasks and actions
  2. Multiple users can now edit large documents simultaneously with new Collaborate Editing Document (CED) feature
  3. Copy and download options added to projects and tasks for more flexibility

All Modules

  1. Updated JavaScript PDF viewer allows more flexibility for previewing experiments and documents
  2. Improved API Key management allows customers to use RESTful APIs more easily and securely.

Scilligence 6.6 Release Notes

ELN 6.6

1. Shared Notebooks
– Users can share notebooks like co-authored experiments
– Owner can rename a shared notebook

2. Improved Formulation Templates

3. Improved HELM functionality
– Support HELM repeating units
– Able to expand HELM nodes
– Improved HELM monomer replacement

4. Summary of plate experiments details
– Thumbnail for plate map
– Display number of assay plates and compounds
– Display submitted assay results

5. Improved audit trail
– Changes to experiment and notebook names tracked
– All witnesses included in experiment export

6. Fixed MF/MW calculations
– Small Library form automatically calculates
– MF updates correctly when structure changes and salt remains

7. User functionalities
– Ability to batch export user information
– No refresh needed when add users, appear automatically in UI

8. Improved re-fitting of QC Curve data in the Dose Response Form

Inventory 6.6

1. 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

2. Bulk Import
– Automatic CAS lookup during bulk import
– User experience improvements
– Ability to create new locations during bulk import

3. New Role – Purchase Stockroom
– Restricted role that can import product/lots/contains and change container location
– Role cannot modify in stock products

4. Access control
– New customization functions such as restriction based on site and department

5. Compound management
– Increased search control
– Improved search display

PMF 6.6

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

Focus 6.6

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

Scilligence 6.7 Release Notes

ELN v6.7.0 Release Notes

  1. Hybrid Free Form – only actual data can be pushed to RegMol.
  2. Improved Registration and Inventory integration
  3. Improved Study Report
  4. Updated Protein Purification template
  5. Improve Curve Assay template
  6. Improve security integration, including OKTA and Azure
  7. New file previewer
  8. Improved HELM features
  9. JSDraw supports Pictures
  10. Able to set colors to individual HELM monomers

6.7.0 Inventory Release Notes

  1. Improved compound management workflow
  2. Improved searching
  3. CAS integration
  4. Improved compound requisition workflow
  5. Improved bulk importing

 Release Notes for RegMol

  1. Improved bulk registration
  2. Improved admin tools on data curation
  3. Improved chirality check
  4. Support parent/batch synonyms
  5. Improved HELM registration
  6. Clean up for HELM-atom/bond hybrid structures


  1. Improved workflow engine
  2. Improved document management
  3. New file previewer


  1. New file previewer
  2. Improved RESTful APIs

Scilligence 6.8 Release Notes

ELN 6.8.0 Release Notes

  1. User FunctionalitiesError ReportingELN FormsDose Response CurveSecurityDisplayGeneral Fixes
  2. Inventory 6.8.0  Release Notes
  3. Compound Management ImprovementsCart ImprovementsContainers ImprovementsCustomization CapabilitiesLanguage ImprovementsAdmin capability improvementCompound Requisition improvements
  4. RegMol 6.8.0 Release Notes
  5. Registration ImprovementsExplorer ImprovementsAssay View and Assay ImprovementsHELM to Structure OptimizationRegMol and Inventory IntegrationAdmin and Security Features Improvement

Scilligence 6.6 Release Notes

Scilligence ELN 6.6.0

  1. Shared Notebooks
    1. Users can share notebooks like co-authored experimentsOwner can rename a shared notebook
    Improved Formulation TemplatesImproved HELM functionality
    1. Support HELM repeating unitsAble to expand HELM nodesImproved HELM monomer replacement
    Summary of plate experiments details
    1. Thumbnail for plate mapDisplay number of assay plates and compoundsDisplay submitted assay results
    Improved audit trail
    1. Changes to experiment and notebook names trackedAll witnesses included in experiment export
    Fixed MF/MW calculations
    1. Small Library form automatically calculatesMF updates correctly when structure changes and salt remains
    User functionalities
    1. Ability to batch export user informationNo refresh needed when add users, appear automatically in UI
    Improved re-fitting of QC Curve data in the Dose Response Form
  2. Scilligence Inventory 6.6.0
  3. CAS Integration and Improvements
    1. Name to structure using CASAutomatic CAS and structure generationUp to date CAS Registration numbersSearch structures via with CAS
    Bulk Import
    1. Automatic CAS lookup during bulk importUser experience improvementsAbility to create new locations during bulk import
    New Role – Purchase Stockroom
    1. Restricted role that can import product/lots/contains and change container locationRole cannot modify in stock products
    Access control
    1. New customization functions such as restriction based on site and department
    Compound management
    1. Increased search controlImproved search display
  4. Scilligence PMF 6.6.0
  5. Improved CED EditingImproved Gantt ChartsImproved Project Member Management
  6. Scilligence Focus 6.6.0
  7. Ability to Synchronize RegMol Assays and ProjectsAbility to Upload Data Using FilesImproved FilteringImproved Sorting for Multiple FieldsImproved SAR AnalysisImproved ChartingAbility to Download Data

Scilligence is now ISO 27001 Certified!

Scilligence Corporation, the leading provider of a unified informatics platform for small molecules and biologics, is now ISO 27001 certified. 

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.We strive to fulfill the expectations customers have in our security standards, and compliance with this globally recognized certification confirms our dedication to protecting data.About ScilligenceScilligence is an innovation leader in web-based cheminformatics and bioinformatics solutions for life sciences R&D. The Scilligence system is built with proprietary technologies to support biologics and small molecules in a unified platform, making it a flexible solution for a variety of research workflows. Scilligence’s informatics solutions include a variety of modules for data management that can be utilized as separate applications or as a fully integrated system. Its tools have been widely adopted by pharmaceutical, biotech, chemical industries, universities, research institutes, and government agencies.

ELN for Academic Research: A Success Story

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.