Category: LabKey Biologics

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.

08 Mar 2017

Quick Look: Assay Data Integration in LabKey Biologics

When developing LabKey Biologics, we wanted to make sure users could not only easily upload assay data, but also easily explore connections between assay data and related entity information.

Trusted Technology for Reliable Data Integration

To support the uploading of new assay data, the LabKey Biologics team took advantage of the robust and flexible assay handling capabilities of LabKey Server to create a mechanism for integrating assay data of all types in the Biologics application. Assay uploads can be automated via the LabKey Server API or done manually by uploading a data file (.xls or .csv) or pasting tab separated values into the interface.

Connecting Data Across Generations

Once loaded into the system, LabKey Biologics presents assay data side-by-side with relevant entity information, even if the connection to that information is several generations removed. This means that, for example, if you are working with a bioreactor run of a particular expression system you can see the relevant expression system when viewing assay data for your samples,  even if there are multiple generations of sample derivations.

We know that this connection is critical when asking questions of your complex data. For example, you might want to see the titer data for all antibodies that contained a specific subsequence, combined with a specific media recipe. This would be very difficult analysis to conduct with spreadsheet based data, but because of the lineage tracking and powerful querying engine built into LabKey Biologics questions like this can be easily answered.

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

08 Feb 2017

Quick Look: Registering Protein & Nucleotide Sequences in LabKey Biologics

In working with our pharma & biotech partners to develop LabKey Biologics, we learned that having the flexibility to register not only nucleotide and protein sequences, but also register a specific DNA/RNA sequence and the protein sequence it encodes was essential.

Sequence Translation Tools

To support this need, LabKey Biologics includes an intuitive mechanism for registering protein and nucleotide sequences on their own (through the user interface or via the API), and performing translations between the two. The key step is our translation page, which gives users the ability to select the encoding DNA / RNA sequence, pick any translation frame, see the resultant protein, and select the start and stop.

Flexibility While Maintaining Uniqueness

The system is flexible to support a variety of scenarios, accounting for the fact that different nucleotide sequences can encode for the same protein sequence and that a single nucleotide sequence can encode for multiple proteins. But at every step ensures that registration is not being duplicated and that entities are 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.

12 Jan 2017

Quick Look: Navigating Entity Types, Entity Lineage, and Connections Between Entities in LabKey Biologics

One of our key goals when developing LabKey Biologics was to make it as easy as possible to find, view, and navigate between different biological entities.

Connected Data for a More Intelligent Search

With this goal in mind, developing an intelligent search engine that allowed users to search based on entity ID, aliases, organisms or even sequences was essential. We also focused on building connections that would make it easy for users to navigate from sequences to plasmids to cell lines, while presenting relevant assay and experiment data at each step. In LabKey Biologics, users can look at a specific protein sequence, and see all the molecules, samples, and assay data connected to that sequence.

Multi-Generation Querying

Exposing these relationships required building a querying engine that could track many, many generations of sample derivation in order to support the data generated during biologic development processes. For example, the extensive processing a transformed cell line undergoes in order to manufacture and purify an antibody target.

Designing for Flexibility

In working with our pharma & biotech partners, we learned that although there are many common elements and terms used to describe biological entities, it’s essential that teams have the ability to customize entity structure and categorization to meet their needs. To provide that flexibility, we designed LabKey Biologics using a consistent visual language to help simplify navigation of these complex relationships with advanced customization options for defining entities and entity relationships.

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

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