Author: Scilligence

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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.

Use Workflow to Streamline CRO Data Management

April 9th, 2024

Collaboration between Pharma/Biotech companies and CRO's has become an essential component of the drug discovery process. Data sharing between collaborators poses significant challenges to the security and efficiency of joint projects. Scilligence will host a seminar to discuss these informatics challenges and present our out-of-the-box solutions to the data sharing problem. The presentation will feature a live demo of three typical example request workflows between the project owner and its CRO partner(s), powered by our scientific informatics platform.

This is a hybrid event, which will be hosted at the Scilligence office in Cambridge (625 Mount Auburn St Suite 203, Cambridge MA 02138. Parking is free.) A Zoom link will be sent to respondents who opt for virtual attendance.

Register Now

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

UIUX

  • 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

ADC/Conjugates

  • 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

Protein

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

Plasmid

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

Registration

  • 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

General

  • 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

UIUX

  • 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

Integration

  • 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

Security

  • 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

Search

  • 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

  • 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.

Workflows

  • Added workflow counts indicator.

UI/UX

  • 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.

Integration

  • 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].

Spring Informatics Workshop (In-Person Event)

April 15, 2024
Catalyst Restaurant

We invite you to join us for an exclusive event at the Catalyst restaurant in Cambridge, MA, for our Spring Informatics Workshop on April 15th, from 10:00 am to 1:00 pm.

At this workshop, we will delve deep into the latest updates on the Scilligence informatics platform, designed to support all drug modalities, including drug conjugates and LNP.

Whether you're a seasoned researcher, scientist, or industry professional, this event is tailored to provide valuable insights and practical knowledge to enhance your workflows.

Here are some highlights you can expect:

  • Updates on the latest features and enhancements in RegMol, our unified entity registration system.
  • Exploration of advanced registration capabilities for various modalities.
  • Partner presentations by industry leaders from Certara and Zifo. 

(Stay tuned for the full agenda!)

Connect with peers, learn from industry experts, and discover how the Scilligence informatics platform can streamline and optimize your research processes.

Space is limited, so secure your spot today by clicking this link or the button below. 

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.