Got Questions? We’ve Got Answers.

Explore our Q&A section to find clear, concise answers about 3RnD. From getting started to advanced tools, we’re here to help you make the most of the platform and streamline your research.

Q&A

Data Management and Security

Where is my data housed?

Your data is securely and privately housed on AWS, encrypted in transit and at rest. You can compare your own compounds to a large library of known historical compounds based on either structure, or based on the biological fingerprints generated by AsedaSciences and our Partners. Keep your compounds and associated data private, while benefiting from the ability to compare to the thousands of compounds screened and visualized by AsedaSciences and our Partners.

How are my compounds kept private and secure?

You can upload and securely store compounds and associated data that are your own, or for a project, a collaboration or an organization. This data is stored in a private and secure instance on AWS that can only be viewed by you and those that are authorized by you, or your administrator. 3RnD employs industry standard cybersecurity measures to support data security requirements.

Who can view my data?

Only you, or those invited by you, or your organization’s administrator, have the ability to view the data you upload, store and visualize. For publicly available or AsedaSciences’ screened compounds and associated data housed within 3RnD, anyone with a subscription may view these compounds.

How are my compounds kept private and secure?

AsedaSciences follows industry best practices when it comes to digital security requirements. While we do not openly discuss our security implementation strategy, we do use the available security tools and follow the security recommendations provided by AWS. We also use 3rd Party security service providers based on industry best practices.

Machine Learning & Artificial Intelligence

How do you use ML / AI within your services?

We use ML to generate our Cell Health Index (CHI), which is a risk probability of a compound being acutely toxic in humans based on measuring its effect on 12 different acute cellular stress parameters. This is accomplished by generating a multiparametric biological fingerprint of a new compound using our SYSTEMETRIC Cell Health Screen and then using ML to compare the fingerprint to a fingerprint library generated from on-market therapeutics, withdrawn and discontinued drugs and known human toxins. Based on fingerprint similarity, our ML algorithm generates a risk probability that a new compound is likely to be acutely toxic in humans. Our approach is similar to using facial recognition or a criminal fingerprint database to identify problem individuals, but instead, we are identifying potential problem compounds. Other ML approaches will be employed across the various different screening data sets that we are generating to help improve prediction across a range of toxicity classes.

Do your ML or AI algorithms use my data?

No, we only use data generated on publicly available compounds by AsedaSciences or our Partners as training sets for our ML / AI algorithms. We do not use your compound structures or any of your proprietary data for the purposes of training or upgrading our ML algorithms. Our algorithms are used to generate risk probabilities for your compounds when they have been run through our screens, but those results are proprietary to you and stored in your private instance.

Will different ML and AI approaches be available in 3RnD?

Yes, AsedaSciences is developing and will make available new ML and AI tools that you can intuitively apply to the data that you have uploaded and stored. Announcements and training modules associated with these tools will be communicated in the future.

How does AsedaSciences approach data quality?

Data quality is central to the philosophy and approach used by AsedaSciences. We believe that high quality data is essential for accurate ML predictions. Poor quality data leads to poor quality predictions. Since our inception, AsedaSciences has implemented rigorous development and Quality Control (QC) practices that we believe sets a standard for cell-based screening methods. Our approach has been to ensure high quality, reproducible data for training our ML algorithms. This level of expectation for data quality is also expected from our Partners.

Screening Services

New Approach Methodologies (NAMs)

New Approach Methods, or NAMs, are in vitro and in silico screening methods developed and validated to help assess toxicity risk associated with chemicals. The goal of developing NAMs is to support the reduction, replacement and refinement of animal use (3Rs) in chemical toxicity risk assessment.

Do the screening services provided by AsedaSciences fall under the definition of NAMs?

Yes, the screening services provided by AsedaSciences and our partners are designed to help predict potential toxicity risk of chemicals earlier in R&D without the use of animals, and thus fall under the definition of NAMs. We use a range of cell-based screens and analytical measurements designed to help predict toxicity risk and improve the selection, prioritization and progression of safer compounds to support 3Rs initiatives.

What types of NAM screening services do you offer?

AsedaSciences, and our partners, offer a suite of validated NAM screening services. The SYSTEMETRIC® Cell Health Screen is a standardized, highly validated, multiparametric flow cytometry-based screen that uses integrated biological fingerprinting and machine learning (ML) to predict acute toxicity risk for new compounds. The ZBEscreen is a zebrafish embryo screen that measures the effect of chemicals across multiple acute and developmental neurotoxicity endpoints at the organ and behavioral level. Biomimetics uses highly validated HPLC based methods to assess properties of a chemical, such as lipophilicity, human protein binding and phospholipid binding which can be indicators of in vivo distribution and a variety of properties that could lead to toxicity. AsedaSciences will continue to expand the range of screens available.

What is biological fingerprinting?

The biological fingerprint of a chemical can be defined as a set of biological signals or features, measured using a standardized method, that when combined, represent its biological effect or fingerprint. When these signals or features are measured using a standardized approach for large numbers of chemicals, the resulting biological fingerprints can be used as a means to compare differences and similarities of their biological effect – both desired (e.g. therapeutic effect) or undesired (e.g. toxic effect). In the case of the AsedaSciences SYSTEMETRIC Cell Health Screen, the biological fingerprints represent the acute cellular stress, or acute toxic effect, of a compound based on measuring 12 parameters of acute cellular stress, across 10 concentrations (100 uM down to 5 nM) of a compound, measuring ten thousand cells individually per concentration. These biological fingerprints for a new compound are then used by our ML algorithms for comparison to a training set of fingerprints from withdrawn and discontinued drugs, known toxins and on-market therapeutics. Based on similarity to fingerprints for known human toxins in our training set, a risk probability of a new compound being acutely toxic in humans can be generated.

Are you open to partnering for increasing your menu of products and services?

Absolutely. We encourage commercial and academic developers of synergistic NAMs, software applications and screening services to reach out to us if they would like to take advantage of the 3RnD platform. We will work with NAM developers to support validation efforts and generate new software applications where needed to provide additional revenue streams. We would like to encourage anyone who feels they have synergy with the tools and services we are providing through 3RnD to reach out to us – we are eager to discuss ways to work together

What types of compounds are included in your chemical and fingerprint library?

The chemical library screened by AsedaSciences consists of 3,000 chemicals across diverse chemical space, classes, targets, mechanisms, status, industries and market segments. For pharmaceuticals, we have compounds across hundreds of targets, mechanisms and diseases as well as on-market, discontinued and withdrawn drugs. We also have screened a diverse set of agricultural and industrial chemicals across various chemical classes and market segments. Our goal is to continue to expand the broad fingerprint library available for comparison by screening diverse compound sets from across all industry segments.

What additional information is available for the compounds you have screened?

All of the compounds screened by AsedaSciences have a “Details” page where annotations are provided based on manual curation of publicly available information (e.g. drug labels) and scientific literature. These annotations are summarized succinctly to provide information that is valuable when conducting nearest neighbor comparisons to support compound selection decisions. Information such as physical chemical properties, target, disease, ADME properties, toxicity information, status and market segments are examples of some of the categories provided. Our approach is focused on providing the key information required for rapid decision making.

Where can we find more information about the various screening methods you provide?

When you register and log in to 3RnD, you will arrive at the “Welcome” page. This contains a series of tiles representing the various features, tools and services that are available. There is a feature titled “Our Biology” which provides a menu containing all of the various screening services provided and a technical description of the method, the biological parameters measured, explanations of normal and abnormal results, analytical approaches and interpretation guides. Descriptions are again designed to be succinct, coupled with illustrations that provide a visual guide of normal versus abnormal for the various biological features measured.

How can we compare our compounds to the compounds in your fingerprint library?

AsedaSciences has implemented cutting edge visualization into 3RnD and there are various ways to compare your own compounds to those screened by AsedaSciences and our Partners. In the Compound Universe, you can visualize and compare your own compounds to those we have screened based on chemical structure or based off the biological fingerprint if your compounds have been run through the same screens. You can also group your compounds or SAR series with compounds from our library by creating “Favorites”, allowing you to create a range of Favorites that can represent chemical series, classes or properties of your choice. Nearest neighbor analysis based on fingerprint or chemical structure similarity is simple and intuitive and provides tremendous potential for accelerating decisions on compound selection, prioritization and progression

Will you be adding more screens to your menu in the future?

Yes, we plan to expand the range of screens available, including new multi-parameter adverse outcome pathway screens based on the same platform developed by AsedaSciences. This will focus on different classes of toxicity. We will also be validating and integrating additional screens from current and new Partners, both commercial and academic

3rd Party Data Sets

Can useful 3rd Party data sets take advantage of your visualization and be added to 3RnD?

Yes, there are many publicly available data sets from various scientific consortia or collaborative projects across different databases that are sometimes difficult to use or interpret, or require software or computational expertise to access and extract useable information. This can be very time consuming. As a result, we will integrate relevant data sets within 3RnD and utilize our visualization tools to make the information accessible and useful for comparisons, particularly where compounds with structures and associated biological data are of value. The data and associated visualizations will be made available at no cost so that scientists within the chemical producing industries can easily and quickly extract value. If you know of or are generating a data set that could take advantage of 3RnD, please let us know or feel free to reach out and discuss further. We are also open to participating in consortia where our platform could be of value and save time and resources.

Will various chemical libraries be available for comparison?

Yes, AsedaSciences is in the process of integrating various chemical libraries for comparison. If you know of a specific library that we have not integrated, but think it would be valuable to do so, please feel free to let us know.