Category: LabKey Biologics

24 Sep 2018
LabKey Biologics Cell Culture Media Development Software Tools

Data-Driven Tools for Optimizing Cell Culture Media

Cell culture is a central component of protein development and the media used during this process can have a significant impact on its performance. In the R&D environment, media technicians are responsible for both the precise production of cell culture media and the optimization of media recipes to maximize qualities such as growth and stability.

Capturing the detailed information about recipes, ingredients, and batches needed to optimize media production is one of the key challenges faced within protein engineering. The advances in cell culture technologies in recent years have quickly outpaced simple spreadsheet and database-based systems for storing media recipes and batch IDs. Today’s media technicians need software tools to consistently structure data about media recipes, ingredients and batches, so it can be easily accessed and queried on demand.

LabKey Biologics provides essential tools to help protein engineering teams overcome key challenges in cell culture media development, including:

Capture the steps, ingredients, concentrations, and other details of cell culture media recipes in the LabKey Biologics software

Detailed Recipe Registration

Registering a recipe in LabKey Biologics allows technicians to specify all of the information needed for its execution including ingredients, ingredient concentrations, steps for creating the mixture, expiration time, and other key aspects. The system also allows the creation of mixtures that contain other mixtures, even when you don’t know all of their underlying concentrations or ingredients (as is often the case with vendor-supplied mixtures).

Media technicians have a number of different methods available for registering media recipes, depending on their complexity and scale. Technicians can create recipes individually using the media registration UI or they can register many recipes at once using bulk upload features or programmatic registration via LabKey Biologics API.

Software tools for creating consistent cell culture media batches.Consistent Batch Preparation

LabKey Biologics helps minimize formulation errors by auto-calculating the amounts for each ingredient in a recipe based on a target mixture amount. As a technician prepares a batch of mixture, they are prompted to input the actual amount of each ingredient used, as well as the raw material ID. If the media technician needs to use multiple bottles of a raw ingredient to fulfill the formulation, the system will allow them to register multiple raw materials for a single ingredients.

Data driven cell culture media optimization using LabKey Biologics softwareFollowing the Media Trail

The structured data captured in LabKey Biologics allows R&D teams to track the complete lineage of each individual sample, and present lineage as a visualization or grid. Sample characteristics, assay results, and relevant media details are tied together allowing media technicians to troubleshoot problematic raw materials, better optimize their batches, and improve upon media recipes to improve protein yield.

With the right tools, cell culture media technicians can consistently produce media batches and iterate media recipes to maximize performance. Request a demo to see this functionality in action and learn more about how LabKey Biologics can help accelerate your biotherapeutic R&D.

27 Aug 2018
LabKey Biologics registration and classification tools for protein engineers

LabKey Biologics for Protein Engineers

LabKey Biologics registration and classification tools for protein engineersThe focus of pharmaceutical and biotech research has seen a significant shift in recent years. Many research teams are no longer driving towards building small molecules, but are instead focused on designing new protein-based therapeutics.

Protein engineers at these organizations are often responsible for the structural design of target molecules as well as the experimental protein production and characterization of their designs. To support this work, protein engineers need software tools to capture details about molecular components such as proteins, antibodies, plasmids and cell lines, as well as the detailed steps of the development process. LabKey Biologics provides an easy to use system for centralizing this information and additional tools to help facilitate protein design including:

Uniqueness Verification

There are a number of entities that might be critical for a research organization to register. These could include:

  • Protein Sequences
  • Nucleotide Sequences
  • Molecules (ex: Antibodies)
  • Plasmids
  • Cell Lines

Each of these entities is checked for uniqueness when they are registered in LabKey Biologics.  This prevents dirty data caused by duplicate records and reduces duplicate work for protein engineers. Uniqueness checks are in place for all entity types, whether you are registering a single sequence or a molecule composed of multiple protein sequences.

Uniqueness checks are also run on data auto-registered during the import of a GenBank file. In that case, LabKey Biologics will register plasmids during the import of a GenBank file, but also auto-register any regions that translate to protein sequences. If a protein sequence already exists, the system will register only the relationship between the plasmid and that protein sequence, not create a new sequence.

Classification

LabKey Biologics includes a classification engine that can identify, predict, and calculate various characteristics of registered molecules. This saves protein engineers valuable time manually assigning classifications.

The system automatically detects many regions and features of protein sequences including leader sequences, variable regions, constant regions, and CDRs. LabKey Biologics can also be trained to recognize additional sequence classifications, for example, by registering a leader sequences as a “Leader” within the system, it will recognize future leader sequences that match it.

LabKey Biologics can also recognize heavy chains and light chains and predict their type,  based on the amino acid sequence of a registered protein, as well as the isotype of the overall antibody.

For all of these classifications, whether LabKey Biologics is detecting subsequences on the amino acid sequence or the type of overall sequences, the protein engineer can always override the classification engine if the prediction is incorrect.

Integration with Other Systems

Often times, protein engineers are using another application to design proteins or plasmids. LabKey Biologics makes it easy to bring this data into the system, either via APIs or by bulk upload. Regardless of the registration method, the same classification and uniqueness checking features apply to all registered entities.

To see this functionality in action, request a demo! To learn more about LabKey Biologics check out our documentation and resources on the LabKey Support Portal.

28 Jun 2018

The Power of Structured Data: Customizing Grid Views in LabKey Biologics

When analyzing the output of an experiment, scientists often need to look beyond the results at related data to answer their research questions. Comparing lineage characteristics like which expression system was used to generate an experiment sample or details about the sample itself, such as the buffer used in it, can uncover crucial data patterns and insights.

This type of data exploration requires data to be captured in a structured manner and integrated into a central system where it can be easily accessed, queried, and analyzed.

Structuring Data for Maximum Value

LabKey Biologics provides tools to ensure that data is correctly structured and consistently stored. For each data type within the LabKey Biologics application, users are able to configure a specific structure, indicating the names of fields as well as their type. Because this data is consistently structured, a user can pull together relevant data from different sources for an integrated view of their data during analysis.

Integrating structured assay and sample data in LabKey Biologics using Sample IDs and look-ups.

For example, when looking at the results for a specific assay type, such as optical density, a user can add details about the samples themselves to the assay results data grid. This might include the buffer used, the expression system used to create it, or the name of the antibody (or other molecule) that was being produced.

Customized Data Views for Quicker Access

Users can customize the default assay data grid view to include these additional look-up columns. Customized default views provide quick access to all the data relevant to the user’s research, instead of having to join data each time they view the dataset. Users can also sort, filter, and search the data in these additional columns the same way they can with native assay data fields.

To see this functionality in action, request a demo! To learn more about LabKey Biologics check out our documentation and resources on the LabKey Support Portal. 

30 Apr 2018
Using LabKey Biologics to integrated data from multiple molecular biology assays

Quick Look: Integrating Data From Multiple Assays in LabKey Biologics

Generating analytical data can be a complex process. It can involve navigating internal and/or external approval processes, hours of experiment planning, and the set-up and use of complex equipment. But even with all of these complexities, the most difficult part of the process often ends up being the analysis of the data in a way that generates meaningful, actionable insights.

Experiment data can get siloed, making it difficult to access, and it often takes different shapes that don’t inherently integrate. Scientists need to be able to join and view data from multiple sources in order to understand how measurements from one analysis may correlate, or be impacted by, measurements from another analysis.

Connecting Assay Data in LabKey Biologics

LabKey Biologics provides powerful querying capabilities that allow teams to join data from multiple experiments and view this data as a single grid or report. This data can then be searched, filtered, and shared just like any other grid of data within LabKey Biologics.

This power is essential when observing the relationship between measures. For example, a team may want to investigate whether or not a correlation exists between characteristics like pH and temperature and observed cell growth in a bioreactor. These measures are collected by different instruments, but they need to be viewed side-by-side in order to conduct this analysis.

Building a Query

Using the powerful SQL Schema Browser within LabKey Server, teams can build and execute queries that combine data from different datasets. One common way to compare assay measures is to join datasets by common Sample IDs. This type of join allows the user to see the measurements from multiple assays side-by-side for each Sample ID. Teams can design and execute queries of varying complexity, comparing two assay measures or many assay measures.

Leveraging Sample Lineage

Users can also query the lineage of each sample and present the parent sample (Bioreactor Run) to which a sample is tied as well as what Expression System entity was used in its creation. Sample lineage provides context for the joined assay data, allowing scientists to easily ask questions and conduct comparisons with other sequences that are seen in different experiments.

Manipulating the Joined Data Within Biologics

Once queries have been created, they operate much like any other grid of data in LabKey Biologics. The results of queries are automatically updated every time new data is added into the system and lineage details like Sample IDs, Bioreactor Runs, and Expression Systems are automatically rendered as links, allowing for easier navigation to details about the entities. Query data grids can be manipulated with all of the standard operations available in LabKey Biologics allowing users to search, sort or filter integrated data. Query data can also be easily exported to allow for analysis in downstream systems.

Ready to see this functionality in action? Check out the quick look video above. For more information, request a demo or register for an upcoming “Intro to LabKey Biologics” webinar.

08 Mar 2018
Integrating analytical data from multiple experiments in LabKey Biologics

Quick Look: Integrating Analytical Data and Understanding Its Context in LabKey Biologics

One of the core challenges laboratory teams encounter is centralizing their data so it can be easily viewed and analyzed in a single place. Without centralized data, teams must turn to time consuming and error prone manual integration methods to derive value from their analytical data.

LabKey Server’s robust mechanisms for defining assays and uploading assay data are helpful for bringing analytical data into a single system, but LabKey Biologics takes this one step further and provides valuable structure and connections that help biologics research teams understand how that analytical data fits into the larger context.

LabKey Assay Designs: Standardizing Analytical Data Structures

LabKey Biologics allows teams to define or customize assay designs (many editable assay design templates come pre-defined within the system) to capture analytical data in a specific structure. Some teams using LabKey Biologics may need to define only a few assay designs to support their research, while others working in a more complex environment may need to define 100+.

When building an assay design, laboratory teams can choose to add fields specific to batches, runs and results to provide additional context for their data. LabKey supports a wide variety of field types (including integer, float, boolean, and text) and users can configure aliases, validation rules, and a variety of other characteristics for each.

Integrating Data Into the System

Once an assay design has been built in LabKey Biologics, data can be added to the system using that design to provide its structure. There are a number of different ways to load your assay data into LabKey Biologics including:

  • Automatically uploading via the LabKey API
  • Manually uploading spreadsheets
  • Pasting spreadsheet-type data
  • Entering data into a form

The first strategy, automatically uploading, leverages the APIs of LabKey Biologics to allow other instruments or file systems to talk directly to the system. The other three strategies involved a manual process suitable for varying use cases. If you have a large spreadsheet to integrate, you might want to use the manual upload method or paste the tabular data directly into the application. If you just have a couple of values you want to enter, simply entering the data into a form in the LabKey Biologics UI might be the simplest strategy.

Leveraging Sample Lineage for Context

As you know, analytical data generated during experiments is tied to a specific sample. Because the lineage of samples is tracked in LabKey Biologics, the application will automatically query sample lineage when data is uploaded and present relevant biological entities side-by-side with analytical data. Showing the sequence or molecule information adjacent to the analytical data, allows scientists to easily ask questions of their data and conduct comparisons with other sequences that are seen in different experiments.

Ready to see this functionality in action? Watch the quick look video above. For more information, request a demo or check out our “Intro to LabKey Biologics” webinars.

17 Aug 2017

Quick Look: Automated Generation of Molecular Species in LabKey Biologics

One of the most common ways LabKey Biologics is used is in researching protein based molecules, often times antibodies. To support this research, LabKey Biologics is equipped with specialized triggers that automatically register commonly seen molecular species when a new antibody is created.

Antibodies and Protein Sequences

When engineering antibodies, the heavy chain and light chain sequences often have signal peptides (or leader sequences) as part of their overall sequence. When these proteins are expressed within a transformed cell line, these signal peptides are cleaved as the proteins are brought out of the cell.

Within LabKey Biologics, when you register a new “molecule” (that is composed of solely of protein sequences), the application automatically examines these sequences to determine if there are signal peptides present. If there are, LabKey Biologics will also register “molecular species” that have the same sequences (and stoichiometry) as the original molecule, without the leader sequences. This is called the “mature” molecular species. Similarly, if the molecule’s heavy chain contains a C-terminal lysine, LabKey Biologics will register a “mature, desK” molecular species that has cleaved the leader sequence(s) as well as the C-terminal lysine(s).

The “mature” and “mature, desK” molecular species are automatically generated and registered by LabKey Biologics. In the laboratory, however, you might detect other molecular species that stem from over-clipping and under-clipping of the leader sequences. LabKey Biologics allows you to manually register these as well, allowing you to connect all of these observed and predicted entities.

New Protein Sequences and Molecule Sets

For molecular species that are automatically generated, their components are often times new protein sequences. These sequences are also automatically generated, along with information about where the sequence came from. LabKey Biologics helps you keep track of those relationships.

Finally, researchers needed a mechanism to refer to all molecules for which the only difference is the leader sequence(s) of the protein sequence(s). For this, LabKey Biologics also automatically assign each molecule to a molecule set. For each molecule in a molecule set, the “mature” molecular species has the exact same components.

For a quick look at this functionality in action, check out the video above. Want to see more? Request a demo or register for an upcoming “Intro to LabKey Biologics” webinar.

25 Jul 2017

Quick Look: Customizing Sample ID Structure Using Lineage in LabKey Biologics

We hear about a wide variety of unique challenges when talking to our users, but one that is very common across many organizations is the difficulty generating sample IDs for new samples. While the requirements for sample IDs vary from research team to research team, a few needs are true for all:

  • IDs must provide context about the sample
  • IDs must be relatively short
  • IDs must be unique
  • IDs must be consistent

To address this challenge, we designed a highly configurable system within LabKey Biologics that allows administrators to specify how sample IDs are “built” as they are derived from other samples or biological entities.

Providing Context

Imagine, for example, that you are creating a variety of bioreactor runs (a specific sample type). As you’re creating the sample IDs to represent these runs, you might want to incorporate the ID of the Expression System (ex: ES-3) into the sample ID that is generated. Additionally, you might want to have the date, the type of bioreactor, and an integer included.

Doing this in triplicate, you’d have a Sample ID structure that looks like the following (where “SF” stands for “Shake Flask”):

ES-3_2017_07_04_SF-1
ES-3_2017_07_04_SF-2
ES-3_2017_07_04_SF-3

 

This sample ID structure would provide information about what is in this shake flask and when the bioreactor was started. In LabKey Biologics, you can easily configure the system to compile a sample ID that includes the values from any relevant fields to help provide context about each sample.

Dates and Counters

Many teams add an integer to their sample ID structure to serve as the differentiator between samples with similar characteristics. To support this approach, LabKey Biologics keeps date counters for each day, week, month, and year so that users can create samples IDs for any time period (past, present, or future) that include an integer is unique within that period.

Always Ensuring Uniqueness

When you generate sample IDs within LabKey Biologics, the application ensures that the ID generation system ensures that all sample IDs are unique. The same is true of Sample IDs that you override manually, or through a bulk upload. If you provide a duplicate in either of these scenarios, LabKey Biologics will flag the duplicate provide you with the option to reject the duplicates or override the existing data. This means that whenever you’re looking at the assay data or lineage connected to a particular sample, the sample ID will be unique.

For a quick look at this functionality in action, check out the video above. Want to see more? Request a demo or register for an upcoming “Intro to LabKey Biologics” webinar.

20 Jun 2017

Quick Look: Requesting and Uploading Assay Data


One could say that the key purpose of any scientific lab is to perform actual experiments. The primary goal of LabKey Biologics is to make sure that the data generated by these experiments is connected to molecular biology entities within the system, but we also wanted to make it simple for teams to request experiments and manage the fulfillment of these requests. By supporting the entire workflow from request to fulfillment to data integration in a central system, teams can significantly streamline their workflows and simplify data hand-offs.

Requesting Work

In LabKey Biologics, within the Workflow tab, teams can create service request trackers to manage different type of work conducted in the lab. These can be trackers for sample preparation, reagent delivery, equipment maintenance – whatever you’d like to track. LabKey Biologics comes preconfigured with a default work request tracker, for managing Assay Requests. This specialized assay request tracker is designed to create a persistent link between requests for assays and the assay data that is uploaded.
Service requests for assays, samples, etc. are requested as part of a parent Work Request. Work requests allow users to group together many different service requests (i.e. different assays, separate sample preparations) enabling a connected view into the work that has been done across the entire project.

The Status of Work

The a user-specific view of the workflow dashboard in LabKey Biologics is presented to each user who logs in to the application. At the top of the page, the interface shows two key lists: 1) all open work that the user has requested and 2) all open work that has been requested of that user. This allows users to see the things that are immediately applicable to them and to take action accordingly. The dashboard view also provides global reporting on the status of all work requests being tracked in the system and and links to any open requests.

Uploading Assay Data

When a requested assay is complete, the generator can easily upload the results directly from the assay request page, and close the activity request, thus completing the workflow. This process also creates a direct link between the completed assay request and the assay data that was generated, making it easy for the requester to access their results.

For a quick look at this functionality in action, check out the video above. Want to see more? Request a demo or register for an upcoming “Intro to LabKey Biologics” webinar.

16 May 2017
Molecule Registration System LabKey Biologics

Quick Look: Molecule Registration in LabKey Biologics

Registering molecules is a key function of LabKey Biologics. In the LabKey Biologics application, a molecule can be any sort of macromolecule, often times an antibody, that is a key target of research.

Registering A Molecule

To register new molecules, LabKey Biologics provides an easy-to-use molecule registration wizard as part of the interface. First, users add a molecule description, aliases, and details about the molecule’s lineage. The second step in the registration process allows users to select the components of this molecule, generally composed of one or more different protein sequences. Finally, LabKey Biologics will make a recommendation about the stoichiometry of the molecule. Users can either accept this recommendation or override it. The application will then verify that this new entity, defined by its components and their stoichiometry, has not previously been registered.

Users can register molecules individually using this wizard, in bulk, or via the LabKey API. LabKey Biologics can also seamlessly integrate with external systems used for antibody design to register entities.

Creating Valuable Connections

LabKey Biologics stores all of the key physical characteristics about registered antibodies and presents users with concise, yet detailed, information about its components and linkage to relevant molecule species, molecule sets, and expression systems.

Following the Path

An expression system is typically generated to produce a specific molecule. This relationship can be seen through the various gene inserts in the construct for a specific expression system, but in LabKey Biologics we’ve built a mechanism to make this connection easier to uncover. When users register a new expression system in LabKey Biologics, the application will make an explicit connection between it and the molecule of interest and then make that connection visible on the entity details pages for easy navigation between the related expression system and the molecule.

For a quick look at this functionality in action, check out the video above. Want to see more? Request a demo or register for an upcoming “Intro to LabKey Biologics” webinar.

17 Apr 2017
Registering Media in labKey Biologics

Quick Look: Media Registration in LabKey Biologics

In addition to tracking the relationships between biological entities and the experiment results from assays run against them, we wanted to give teams a way track the composition and steps taken to create each sample as well as provide a tool for creating and storing recipes.

Building Media Recipes

We built into LabKey Biologics a straightforward mechanism for registering new media recipes that allows team members to specify which ingredients will be used, the concentrations of those ingredients, the steps that need to be taken to prepare the mixture, and the target yield.

When selecting ingredients to include in a media recipe, users can select from a list of preloaded ingredients that are defined by their lab. They can also use other mixtures as ingredients in a mixture.

Creating a Batch

When it’s time for a team member to create a batch of a particular recipe, they will specify the desired yield and LabKey Biologics will automatically calculate the quantity of each ingredient needed to achieve that yield, based on the mixture recipe. As the user adds ingredients according to the recipe, they will indicate in the interface the actual quantity and the specific raw material added to the batch. Raw materials are the physical manifestations of ingredients and are registered in the system with their unique lot numbers. Registering not just ingredients, but also specific raw materials, helps keep track of laboratory supplies used and allows teams to investigate the downstream effects of different materials.

Following the Media

Media recipes and batches are treated like any other entity within the LabKey Biologics system, meaning that the lineage of samples can be traced back to any applicable media. This allows scientists to investigate the impact of different recipes, different batches, and even different sources of supplies on protein production.

For a quick look at this functionality in action, check out the video above. Want to see more? Request a demo or register for an upcoming “Intro to LabKey Biologics” webinar.

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