Behind the Code: Exploring Scilligence’s Software Design

April 1st, 2024

In this blog post, we wanted to walk you through the software design philosophy at Scilligence. We pride ourselves on three “pillars” — client needs, industry trends, and market gaps — as fundamental to our success. Collectively, these pillars help us gain a comprehensive understanding of, our clients, the marketplace, and our competitors. They are inter-related and have helped us to make strategic decisions leading to long-term success.

Client Needs
Understanding client needs is the best way for us to keep pace with your demands and to manage short- and long-term expectations (surrounding the same demands):

  • Crucial Feedback: Client needs are what got us started in this space! By listening to your suggestions, problem areas, pain-points, and overall feedback, we gain insights to improve our offerings. Listening to your feedback has helped direct our focus towards improving our products and offerings — this can involve anything from bug fixes, optimizations, to upgrades and entirely new features. It is tremendously helpful to us as it lets us know what to do for you.
  • Stronger Relationships: We foster trust and loyalty by listening to our clients to ensure you feel heard and understood. We take the time to listen as we value your business and your input to create a positive and engaging relationship. This leads to better products and services, happier clients, and a more successful business overall.

“A fundamental belief at Scilligence” Tony Yuan, Director of R&D says, “is that we listen to our clients. Why? Because our business would not exist without them. We need them to be successful in every regard.”

Industry Trends
Analyzing industry trends is critical for us to thrive and here's why:

  • Informed Decisions: Analyzing industry trends has helped us make data-driven choices. We apply this principle to everything from product development to marketing strategies. Perhaps there is a rising demand for a feature that we have not offered before, or a new function that can help make data analysis faster and easier. A good example of this is the Antibody Drug Conjugate form in RegMol (which is our registration software). We built this function from the ground-up with the idea that users will prefer to register the individual components of an ADC and then use them to “piece together” or assemble the ADC itself. Being aware of these trends helps us to not only identify new opportunities but also identify areas for growth and improvement as well.
  • Adapting and Evolving: As the scientific community makes new discoveries that increase our understanding of biological processes, there is a need for informatics solutions that accommodate the new paradigm. We are constantly analyzing trends, so we can stay informed about the latest developments and ensure that our offerings are relevant. We innovate and adapt, manage risks, and stay competitive to keep pace with the changing landscape.

Staying updated with industry trends is a critical aspect of our software design philosophy as it empowers us to make informed decisions, plan our roadmap, and be industry pioneers. All of this helps us stay on top of our game and get the best products out to you.

Market Gaps
We see market gap analysis as a vital process for our software design because it helps us uncover hidden opportunities for growth and success. They represent opportunities for us to innovate, optimize existing offerings, or develop new ones to better cater to your unaddressed needs.

  • Unmet Needs: Market gaps represent areas where client needs are not being fully satisfied by the current informatics market. By identifying these gaps, we develop innovative solutions so that we can address unmet needs. In some cases, this has led to entirely new product offerings such as the formulation workflow for designing lipid nano-particles (LNPs).
  • Building Client Base: By filling a market gap, we have been able to serve a new pool of potential clients who were currently underserved. In fact, this has been the driving philosophy that perfectly blends features and functions across a centralized, unified platform that clients were previously “cobbling together” from disparate options.
  • Competitive Advantage: Addressing a market gap also gives us a significant edge over our competition. We were the first ones to build the HELM Web Editor in collaboration with the Pistoia Alliance. We have pioneered this technology that effectively fulfills the unmet need of representing macromolecules. At the same time, we have captured a loyal client base long before our competitors who are only now entering this space.

Analyzing market gaps informs us where to focus our attention and what features and functions to develop and has allowed us to distinguish ourselves from the competition.

In conclusion: Industry Trends + Client Needs + Market Gaps = Solutions that work for you. By bringing these three elements together at Scilligence we have developed a strong understanding of our target market and have positioned ourselves to offer solutions that truly resonate with our clients.

RegMol 7.2 External Release Notes

March 15th, 2024

Assay Protocols and Views

  • Protocol columns (admin feature): Can use a dictionary list for the items list when using select column type
  • In Add Assay Results page: The ability to Hide Blank columns in this page can be added with a configuration
  • Protocol columns (admin feature): The Assigned Protocols column has been moved to a child table to improve the usability and space management of this table
  • Assay View function change: When using the Download All function to download assay view results to CSV or SDF, the user must click the save button first to save the assay view
  • Assay View: removed limitation on upload of more than 1000 entities

Cross-application Integration

  • Registration and Inventory database and GUI alignment: Registered entities in RegMol and the corresponding Products, Lots and Containers in Inventory are synchronized.
  • Swagger page/API key additions and general improvements
    • Plate Maps list and save
    • Parent check will recognize invalid structures and return a message


  • Improved messaging:
    • In an integrated system (ELN or Inventory integrated with RegMol) if a user or project does not match in one of the apps, the pop-up message will indicate which app is causing the permission block when pushing entity information
  • Improvements to language detection:
    • The system can now recognize an Entity Type if written in Chinese characters
    • Improvements to Chinese and Korean characters display in CSV downloads from the Cart page
  • In the RegMol Cart Parent and Batch ID's are now clickable links to the entity page
  • General text visualization improvements when using Dark Mode
  • Admin Feature: A full-screen option is added to Structure Editor in the Update Structure/Sequence dialog to allow better visualization of larger sequences/structures
  • The structure views are harmonized across RegMol for example in the Cart page and Project Portal structure images will display as the same size
  • Parent Entities MW column: Improvements to MW display so that the numbers are now right justified
  • UI clean up
    • Removed unnecessary icons
    • Replaced grid filters with column sort

Search and Explorer

  • Improvements made for:
    • Query speed
    • Standardizing Search types e.g., adding atom level search to Advanced Search

HELM and Enumeration

  • Improved messaging for denoting special characters in HELM monomer symbols

Entity Types


  • Streamlined entity forms by removing unnecessary fields
  • Bulk upload improvements by aligning Single and Bulk Registration mapping fields
  • Informational messaging improvements for ADC component connection registration process
  • Provided capability to register No-Structure ADCs. Three use cases:
    • No Structure at all
    • No Sequence Antibody
    • No Payload Structure


  • Translate and display the amino acid sequence of a highlighted coding region of DNA entry


  • Added the ability to update a parent sequence using the Admin> Data Management> Update Structure/Sequence


  • Added more size unit options for containers
  • Parent Explorer page: Ability to add Custom Column filtering (with configuration)
  • Registration Form UIUX: For an existing compound having an External ID, the External ID field is empty on the registration form when creating a new batch
  • Registration UIUX improvement: When sorting by Parent under the Project Portal user can choose to show only parent entities (with configuration)
  • Added the ability to allow RegMol users with Manager privilege to edit an entity registered by another user

ELN 7.2 External Release Notes

March 15th, 2024


  • Admin level Instruments page and the Materials page: The count function is optimized
  • Additional API documentation added to Swagger page
  • Added ability to use special characters (@, #, &, etc.) in Project names
  • Improvements in Project Shared Folder functionality


  • The layout of pages with navigation trees is enhanced by aligning tree and table headers
  • Improvements in the readability of Information and Error messages
  • The placement of menus and dropdown menus will auto adjust to the screen space
  • Improvements to page navigation by scroll bar
  • Improvements to table filtering options
  • Improvements to Small Card view on Main page
  • Improvements in ELN labels translation to Chinese characters
  • General icon fixes


  • Improvements to the Choose Availability connection between SSR form and Inventory
  • Single Dose Screening form: Improvements to Plate naming in ELN form and name tracking in RegMol Assay database


  • Enhanced login functionality for users with multiple accounts on page time-out
  • The Copy Experiment icon in the Main List page can be hidden (with addition of a configuration key) upon request
  • Project security is added by default for Co-Author feature

Experimental Templates

  • My Reagents feature improvements: can process and display larger Macromolecules and Polymers
  • Protein Expression: improved disulfide bond addition and display
  • Weigh Station connection improvements
  • In pre-formatted text Free-Form templates, the option to clear text  in “yellow text” area has been enabled
  • Time stamp added to experiment creation date
  • Decimal points for density calculation can be adjusted
  • Single Step Reaction: Can now capture temperature and time ranges in procedures 
  • Flex form: Table of contents added
  • Added Audit Trail information to PDF downloads
  • In text areas where checkboxes are added, a preferred checkbox indicator can be customized


  • Improvements to searching within nested experiments for non-admin users
  • Added ability for searching titles with special characters
  • Improvements to Fuzzy search capabilities
  • Improvements for searching with Chinese characters

Inventory 7.2.0 External Release Notes

March 11th, 2024


  • Location types are now dictionary defined and can be editable for admins from the settings menu.
  • Location changes can be reverted.
  • UIUX improvements to Location tree display (OK Button).
  • Location Page should only show containers with location (when clicking root location).

Products, Lots, and Containers

  • Added expired days filter on lot level.
  • Low amount indicator on locations page now supports mass units.
  • Streamlined Plasmid form, removing unnecessary fields.
  • Improved messaging to indicate when there is insufficient quantity to perform a split
  • Allow multiple packages in one grid cell location.
  • SDS field changed to upload file type by default.
  • Chemical Lab Safety link can be enabled on request with a configuration.


  • Added workflow counts indicator.


  • First row in containers table is automatically selected if there is only one item.
  • Show Progress animation on Container table in all pages besides Products page.


  • RegMol and Inventory integration improvements- Actions in one app are mirrored in the other.
  • History pulls from RegMol to Inventory when apps are integrated.

Exploring the Versatility of Lipid Nanoparticles in Drug Discovery

February 21, 2024

Lipid nanoparticles (LNPs) have emerged as a compelling drug delivery system, offering significant advantages. Today, we'll delve into what makes LNPs so intriguing and explore why they are gaining traction in the pharmaceutical industry.

Advantages of Lipid Nanoparticles:

  1. Targeted Delivery: Surface motifs allow for targeting specific cells and with this targeting capability you can reduce off-targeting effects so there'll be less side effects to your drug and less drug would be needed.
  2. Great Half-Life: Oftentimes the nanoparticles will have a polyethylene glycol (PEG) serface modification which will allow for immune cell evasion.
  3. Payload Versatility: LNPs are able to carry multiple types of payload, including mRNA which often undergoes degradation in the body. Nanoparticles can protect this cargo from degradation, allowing for a therapeutic that would usually be challenging to use.
  4. Enhanced Cell Uptake: They have improved cell uptake, and with that you can control when the drug is released so you can allow the nanoparticle to be uptaken by the cell and then release the cargo once it's in the cell

Moreover, the endorsement of LNPs by the FDA is exemplified by the successful deployment of COVID-19 vaccines developed by Moderna and BioNTech/Pfizer.

LNP Experimental Workflow Captured in ELN:

  • LNP Components: LNPs are composed of a lipid mix. Most commonly is nucleic acid payload. The lipid mix can include an ionizable lipid, phospholipid, helper lipid, and stabilizer lipid. Several include cholesterol, or a modified cholesterol, but doesn't necessarily have to include all those.
  • Preparation Methods: LNPs are very modular and so they can be mixed, matched, and modified. You can have the same components but adjust how the formulation is made and it’ll result in a very different nanoparticle that may have different characteristics that you're looking for. You could adjust the size, the surface potential, any motifs on the surface of the nanoparticle, all to try to meet your need and provide a good drug delivery system.

Scilligence ELN Approach:

At Scilligence, our Electronic Laboratory Notebook (ELN) offers comprehensive support for LNP design and development:

  1. Capability to design empty and loaded lipid nanoparticles
  2. Our system offers two distinct calculation approaches and they vary based off of the values that the user would have to enter
  3. Ability to handle multiple ionizable lipids and APIs in the nanoparticle design
  4. Retrieve component information directly from your Scilligence RegMol. Just like with the ADC you can register your components so all of your lipids and your RNA using HELM and being able to pull that into ELN to design your lipid nanoparticle
  5. Ability to register your lipid nanoparticle directly from ELN - Available in Version 7.3
  6. Track assays and stability with our suite of apps (ELN, RegMol, and Inventory) - Available in version 7.3

Here is a short ELN demo showcasing the LNP mole% form:

If you have any inquiries regarding how we can enhance support for your scientific workflows or any of our modules, please don't hesitate to reach out to us at [email protected].

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,, 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

RegMol 7.1.0 External Release Notes

March 11th, 2024

UI/UX Improvements

  • Improvements to drawing editor icon display
  • Added tool tips to peptide enumeration function for improved usability

Assay Protocols and Views

  • Assay Views: Improvements to result sorting order and consistency in downloads
  • Added Assay view ability to show residual standard deviation (RSD %) values alongside average of IC50 assay results
  • Added Assay Protocol ability to show other values of Inhibitory Concentration (IC) along with IC50 in the same assay protocol
  • Assay Protocol: Added Next and Previous buttons to improve navigating between individual data results

Cross-Application Integration

  • Improvements to database data storage and access for data push from ELN to RegMol
  • Improvements to database data storage and access for data pull from RegMol to Focus

Registration Improvements

  • On parent and batch registration pages, added configuration options for hiding and adding features
  • Improvements to Parent attachment table data capture and storage
  • Improvements to the default uniqueness check for entities with form types that do not use a drawing editor
  • Improvements in audit trail information capture in entity history
  • Improvements to the data capture and display for SDF file entity headers when downloaded to SDF file
  • Improvements to information message error notification when registering an entity batch to a different entity type than the existing parent, the message will include the existing parent type and ID
  • Added rule for stripping solvates for entity registration and bulk upload
  • Added check parent function for protein sequence in bulk register
  • Information message improvements when inadvertently mapping the same field twice in bulk upload
  • Added feature to allow a user other than owner or admin to edit an entity batch
  • Improvements to parent synonym data capture using bulk update
  • Added feature to allow an entity registered from ELN to be edited in RegMol by any coauthor of the ELN experiment
  • Improvements to information message during bulk register mapping if two columns are being mapped to the same field in error
  • Added ability for a zero solvate ratio for capturing trace or unknown amounts of solvate
  • Improvements to process for adding custom fields

Search and Explorer

  • Added display of Parent Name to the Parent Explorer page
  • Improved usability in advanced search results where hovering over entity type icon will display the name of the entity
  • Improved search performance by allowing exact match for parent or entity ID
  • Improved stereochemistry structure search by using Cahn–Ingold–Prelog (CIP) priority system designations

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