5 Electronic Lab Notebook Features Scientists Can’t Live Without

ELN features An ELN (electronic lab notebook) is an essential software tool for documenting experiments, reviewing compiled results, detailing meaningful conclusions, and collaborating with team members. As scientists work with increasing volumes of data, concerns over data reproducibility, data integrity, intellectual property and security/compliance have led to the wide ELN adoption in nearly every scientific discipline. Once viewed as little more than a paper-on-glass/word-processing application, ELN features have grown to meet the complexities of modern-day research. Below we outline some essential ELN features to look for when evaluating an electronic lab notebook for your organization.

ELN Feature Areas to Consider:

1- Ease of use
The ELN you choose should be easy to use and implement. This is especially critical in driving adoption within the organization. That means the user interface should be intuitive for common functions. Ideally, your new ELN should not require extensive training to learn nor require sophisticated integrations with other software to be useful.

2- Templates
The ability to create and use templates of common notebook forms saves time by reducing duplicative work. The ability to quickly modify templated entry types is an essential feature for saving time and improving overall work satisfaction. By creating templates for specific scenarios such as purifications, cell passaging, or repeated analytical work, your team can save time and standardize the formatting of notebook entries.

3- Data Links/Connection
Compiling data for meaningful write-up and conclusions should not require a huge investment of time and effort. By far the easiest way to surface data is for your ELN to have direct access to your underlying data management system that captures the data. This puts your relevant data at your fingertips while authoring and only external data will require effort to incorporate. Directly referencing data not only saves time, it also promotes data integrity and ensures that valuable data remains at the forefront of the decision-making process during the R&D lifecycle.

4- Attachments and Images
External files and images are important components of complex workflows. It should be easy to incorporate them into notebook entries in various formats such as pressure traces, spreadsheets, images, CoA’s or other QC documents, and SOP’s. The ability to bind these files with your signed notebook contents and view the attachments with a notebook entry can also be a huge time saver.

5- Collaborative Features
In the highly collaborative research environments of today, it is essential to have an ELN that makes it easy to work with other contributing scientists. The ELN should support collaborative authoring and a streamlined sign-off/review process for notebooks. It should be easy to find the notebooks that need your attention, comment or review. You should also receive reminder notifications for these actions when you aren’t in the application. These collaborative features facilitate important discussion and encourage timely and accurate documentation of work.

About the Biologics LIMS ELN
Biologics LIMS includes a full-featured electronic lab notebook seamlessly integrated with the Bioregistry, Assay Data and Workflow Management tools. This user-friendly ELN allows scientists to:

  • Save time authoring and reviewing notebooks with templates, notifications and an intuitive interface
  • Highlight valuable data by linking directly to bioregistry entities, samples and assays
  • Collaboratively document and discuss notebook entries and referenced data

Click here to learn more about LabKey Biologics.

What is a bioregistry?

From cell lines and constructs to their vectors and insert sequences, biotherapeutic development involves many moving parts that need to be defined and connected. Using spreadsheets to manage this data and their inter-relationships is a highly inefficient and error-prone endeavor. Without a central bioregistry to capture and track all of these pieces, researchers could end up with data that is inaccurate, redundant, and insufficient. 

A bioregistry is a structured data repository that helps scientists answer a multitude of questions during the biotherapeutic development process. By efficiently attaining answers to those questions scientists can make data-driven decisions, increase efficiency, and trust the integrity of their data. Time is precious in biotherapeutic development and reducing duplicative efforts and time wasted in finding entity information can be highly advantageous to most organizations. 

Adopting a bioregistry can provide biopharma organizations with the following benefits:

What is a bioregistry?

  • Centralization of information for critical biological entities and protection of intellectual property
  • Eliminating duplication and improving data integrity by verifying the uniqueness of entities upon registration
  • Creation of links between samples, entities, electro nic lab notebooks and entity creation processes (protein, expression, purification, characterization)

The LabKey Biologics Bioregistry

LabKey Biologics includes a fully integrated bioregistry as part of a suite of integrated software tools for biotherapeutic development. The bioregistry captures complete entity and sample information for molecular entities, nucleotide sequences, protein sequences, expression systems, constructs, vectors and cell lines. Researchers can easily navigate through entities and their relationships. For example, researchers can find a specific molecule and see the component sequences, the samples of that molecule and the assay data associated with those samples.

Click Here to learn more about LabKey Biologics and take a tour!

Developing the Biologics ELN with Just-Evotec Biologics

For many scientists, documenting ongoing research and experiments in an electronic lab notebook is an afterthought. Often times this is due to a perceived lack of features and general dissatisfaction with the ELN being used. It is this situation that led the team at Just-Evotec Biologics to go on the hunt for a new electronic lab notebook. The effort was lead by Tara Kulas- a scientist in the High-Throughput Analytical Sciences Group at Just-Evotec. Also responsible for managing the company’s current ELN, Tara was all too familiar with the challenges her team was facing. Drawbacks of their current system included a lack of integration with existing data and workflows and limited functionality related to attachments and the sign-off process. 

After evaluating three different ELN options, Tara and the team at Just-Evotec decided to partner with LabKey to build a modern “data-connected” ELN that fully met their requirements. Among other improvements, the  Biologics LIMS ELN provided:

  • Ability to reference bioregistry data, samples and other notebooks 
  • Addition of attachments, inline images and tables within notebook entries
  • Simple and modern user interface with streamlined sign-off/review

Tara shared her search for the perfect ELN and key features of the LabKey Biologics ELN at the 2020  LabKey User Conference in her presentation titled – “The quest for an ELN we actually want to use.” Watch the presentation below:

Data Management for Precision Oncology at OHSU

The Knight Cancer Center’s Precision Oncology program depends on the complete, correct, and integrated collection of clinical and research data. LabKey handles the data so that researchers can focus on treatments and patient care.

The status quo for cancer treatment is to assign a standard treatment based on the type or location of a patient’s cancer. Past performance of treatments is aggregated and evaluated based on general effectiveness for an average patient. This approach does not take into account the uniqueness of a patient’s tumor on a genomic, structural or microscopic level. 

Precision oncology by contrast uses a targeted approach that takes into account the individual characteristics of a patient and their cancer to create specific treatment recommendations tailored to the individual patient.   By collecting large amounts of data, oncologists are able to analyze fine-grained details about the performance of specific treatments and patient attributes to improve the outcome for the individual patient. 

Managing Precision Oncology Data

Managing the vast amount of data required for precision oncology can be a challenging task for researchers. Having a myriad of spreadsheets with multiple owners or trying to collect and analyze data that is siloed in disparate systems can be detrimental to gaining a complete understanding of a patient and their cancer.

LabKey provides research data management tools that are highly tuned to bring together the diverse datasets and offer alignment and reporting.  With LabKey, the OHSU Data Management Systems Team makes the data Findable, Accessible, Interoperable, and Reusable to facilitate clinical decision-making and research discovery/hypothesis testing and generation. 

LabKey Server for Precision Oncology Data Management at OHSU

LabKey Server is at the heart of the Knight Cancer Institute’s data management system. Led by Patrick Leyshock Ph.D., the Data Management System Operations Team at the Knight Cancer Institute is responsible for designing, implementing, and maintaining both technologies and work processes for precision oncology data management. The presentation below focuses on the Knight Cancer Institute’s LabKey-based precision oncology data management system and covers multiple aspects of the system, including its architecture, workflows, and user types.

Benefits of Sample-centric Freezer Management Software

Most freezer management software aims to be a mirror image of a lab’s freezer space. Samples are assigned location in the freezer at the same time as they are entered into the system, and removed from the system when they are no longer in storage. Although this may be helpful in managing freezer capacity and sample locations, this “mirror image” approach does not always accurately reflect lab workflows or provide a full chain of custody of a given sample. 

In many labs, samples are transported, received, and processed before they are stored. Similarly, samples can also be completely removed from storage, but their data and audit logs may need to persist in the system. The freezer management software described above would be ill-suited to handle both of these scenarios. To fully track a sample and provide an end-to-end history, teams should search for a sample-centric freezer management tool- one that separates a sample’s existence from the physical location in which it’s stored.

A sample-centric freezer management software has the following benefits:

1. Samples can exist outside of a storage framework. This means that teams can:

  • Save time and improve visibility of work by registering samples before they arrive
  • Easily view consumed, expired or shipped samples without crawling an audit log
  • Track chain-of-custody of samples that are never meant for storage

2. Samples can be part of lab tasks before or after they are physically stored. This is useful in cases like:

  • Pre-registered samples are part of a “Receiving” workflow job
  • Sample processing can be tracked in the system before adding the samples to storage
  • Outgoing samples can be tracked in a workflow job

3. Experimental data can be associated with samples at any time. This benefits teams by:

  • Adding associated data from external sources to be registered with samples, regardless of storage status
  • Removing the need for “staging” freezer space to make updates to samples and their experimental data
  • Creating a single space for tracking samples and their associated data, whenever it is available

About LabKey Sample Manager

LabKey Sample Manager includes a sample-centric freezer management solution into the application. This means you can create samples, add metadata and lineage information, perform work and even upload assay data — all without being required to have your sample in freezer storage. Freezer management in Sample Manager can help you:

  • Manage your freezer with an end-to-end sample tracking system that stores the entire sample history and chain of custody in one place
  • Organize your samples using a customizable structure that accurately reflects the physical freezers in your lab
  • Track samples in and out of the freezer (freeze/thaw counts) and automatically calculate and track changes in sample volumes
  • Easily find samples in the freezer and move samples between freezers
  • Tracking and maintaining full audit logs of the freezer and of the samples

What’s New in LabKey Server 21.3

LabKey Server

  • Ontologies IntegrationControl vocabularies and semantics using ontology integration.
    • Browse the concepts in your ontologies and add concept annotations to data. 
    • Use an Ontology Lookup to map entered information to preferred vocabularies.
    • Additional SQL functions and annotations.
  • Option to merge changes when importing dataset data. (Also available in 20.11.3)
  • Dataset audit logs provide a detailed view of what data has changed
  • New Assay Type Selection Interface – Simplified method for selecting a Standard assay (recommended and most common), vs. one of the Specialty assays. 

Sample Manager

  • Freezer management has been added to Sample Manager. Key features include:
    • Match digital storage to physical storage in your lab with configurable freezers.
    • Easily store and locate samples from anywhere in the application. 
    • Track locations and chain of custody of samples. 
    • Check in and out, record amount used, and increment freeze/thaw counts. 
    • Easily migrate from another system by importing sample data simultaneously with location data
  • Improved sample import includes removal of previous size limits on data import, background sample imports, and in-app notifications when background imports complete.

Biologics

Premium Resources Highlights

Release Notes

See the full Release Notes 21.3 (March 2021)

Sample Management for the Growing Lab

For many laboratories, growth and the changes that come along with it can be both exciting and challenging to sample management operations.

Without careful planning and forethought about sample management, even the most organized lab down can go down a spiral of compounding challenges. Misplaced samples, lapses in data integrity, and confusion on workflow steps are just a few of the difficulties that may arise when a laboratory is experiencing growth. A lab undergoing “growth” may be:

  • Processing a higher volume of samples overall or a higher volume of a specific type of sample
  • Implementing new sample processing procedures, experiments, and data collection methods
  • Expanding their existing operations and the laboratory staff needed to support changes

In this webinar, we present five real-world strategies to help your lab get ahead of the challenges you may face. These include:

  1. Change is difficult- be flexible!
    A growing lab will experience many forms of change. Be flexible and ready to adapt at every stage.

  2. Plan for your metadata and sample tracking needs.
    Keep the sample information needed for accurate tracking at the forefront of your planning. As your lab grows, the data you need to capture may change.

  3. Don’t let your freezers get out of control.
    As your sample storage needs change, be sure to prioritize freezer organization from the start.

  4. Standardize your lab processes.
    By taking even small steps toward standardizing processes, labs can optimize their efficiency and ensure a smooth evolution.

  5. Research sample management systems.
    Choosing the right (or wrong) sample management system can have a lasting impact on your lab.

With preparation, your lab can successfully navigate change while improving the productivity and efficiency of your sample management operations. Watch the webinar below:

LabKey Sample Manager is an easy-to-use sample management software designed to help labs efficiently track samples, define laboratory workflows, and unify samples with assay data.Sample Tracking with LabKey Sample Manager

Sample Tracking – End-to-end sample tracking features including chain-of-custody tracking,  sample types and sources, and lineage views

Freezer Management – Flexible and intuitive management of freezer capacity and sample storage locations.

Sample Data Integration – Integrate assay data with your samples and assign metadata for a complete picture of your ongoing experiments

Sample Management Workflow – Assign samples to user-defined workflows and monitor the workflow completion status at each stage for every sample

Explore Sample Manager – register to take a product tour!

FDA MyStudies for Decentralized Clinical Trials

Decentralized clinical trials (DCTs) expand options for trial participation by populations who are unable to leave their homes as easily or frequently as is required for traditional clinical trials. They can also help clinical trials do a more thorough job of accessing diverse populations by reducing geographical barriers, increasing trial enrollment, and improving retention. DCTs can also assist in capturing participant-centric data outside of the medical setting such as medication adherence, exercise, quality-of-life metrics, and other pertinent data. Although decentralized clinical trials have recently taken the spotlight as a remedy to challenges brought on by the COVID-19 pandemic, they will likely continue to be a widely used tool in clinical trial studies. 

Mobile Apps for Decentralized Clinical Trials

Mobile apps in particular have the potential to increase the efficiency and reach of prospective studies. One notable example is FDA MyStudies. The FDACOVID MyStudies selected Harvard Pilgrim Health Care Institute (HPHCI) to lead the development of this mobile application to facilitate the collection of real-world data directly from patients to support decentralized clinical trials, observational studies, and registries. Harvard Pilgrim selected LabKey as their development partner tasked with building a secure back-end storage environment for collected data. LabKey was selected due to the platform’s flexible, science-specific architecture. With the project’s long-term goal of expanding the use of real-world data across research programs, the application framework needed to support a broad range of potential healthcare topics through configuration as opposed to requiring development for each new project. LabKey Server also stood out as an ideal solution because of the platform’s ability to handle PHI/PII data in a manner compliant with HIPAA and FISMA regulations. 

The primary goal of the project was to build an open-source reusable platform consisting of a mobile device application and patient data storage environment that fulfills the FDA’s regulatory needs regarding data security and traceability. Creating a platform that meets regulatory data security and privacy standards while remaining extensible to different types of studies and patient cohorts was central to the requirements and design of the platform. The FDA MyStudies platform can be used and rebranded for studies in other various therapeutic areas and has most recently been modified to enable contactless patient informed consent during the COVID-19 pandemic.

For more information on FDA MyStudies for decentralized clinical trials, please see below:

FDA MyStudies Case Study

Publication: The FDA MyStudies app: a reusable platform for distributed clinical trials and real-world evidence studies

Upgrade Your Freezer Management System Without the Pain

Migrating data from a freezer management system can be hard. So difficult in fact, that many labs continue to use an outdated system long after it is no longer serving their needs. Sometimes, the legacy system has even become a hindrance to sample management operations. However, this shouldn’t deter you from taking on the challenge of upgrading your freezer management software and reaping the rewards of improved organization and management of your lab samples. Below are a few tips for a painless switch to a new freezer management system. 

Freezer management systemPlan and prepare for your new freezer management system.

Develop a plan for migrating to your new system that includes a timetable for which freezer data will be migrated, and roles/responsibilities during the process. Make that your team is trained on the new system and that you are communicating clearly throughout the process.

Backup your legacy data. 

Before anything, it’s important to have a backup of data for record-keeping and disaster recovery. During the migration process, this backup will serve as a record of your legacy system data- some of which may not transfer over to the new freezer management system. Create system-wide backups for recovery, but also human-readable backups for data mining if an unlikely event happens. 

Determine what will be migrated.

Take this as an opportunity to clean up legacy data and items in the freezer. This might even be a good time to defrost and clean your freezers if they are not on a regular defrosting schedule. Focus on the essential samples and related data to keep your system and your freezers clutter-free. For each sample type, determine the list of fields exported from the legacy system and how they will map to the new system. Document data types, field validation (required fields or a specific range of values), and any other requirements such as relationships between samples and sources.

Utilize your resources – ask for help. 

Many vendors offering freezer management system offer migration services, so ask for help! If the system you’re moving to doesn’t offer this, consider hiring a consultant or contractor to help if your team members are too busy or you need advice. When choosing a system, make sure to consider the support you will need to implement your new system.

LabKey Sample Manager provides:

  • Easy, straightforward data import format to register your samples and their locations in a single step
  • Unlimited user-defined fields allow teams to capture any data necessary
  • Migration services and customer support when needed

Click Here to learn more and take a tour!

LabKey Supports for NIAID COVID-19 Immune Response Consortium

Since the start of the COVID-19 pandemic, the urgent need to gather, harmonize and share data has been felt across the scientific research community. To meet this demand, the NIAID Immune Response Consortium developed the HGRepo Informatics Framework in partnership with LabKey. This informatics system centralizes unstructured and de-identified clinical data collected from 14 domestic and international hospital sites. Researchers are using this data to study host genetics, host response, and microbial genetics as they relate to COVID-19. Downstream data from their research includes gene expression data, single-cell multi-omics data, humoral signature data, serology and more. 

Support from LabKey

LabKey supports NIAID by providing a platform to link all of the generated data back to the original clinical, demographics, and phenotype data. By helping integrate, track and make data accessible for collaborative research and integrated analysis, LabKey is helping researchers to quickly get the most insight from the consortium research data. In short, LabKey Server provided a central data repository to provide standardization and structure to clinical data including:

  • Definition of Dataset and Sample Properties
  • Controlled Vocabularies 
  • Categorical Data Groupings
  • Reports and Views
  • Automated update of links to Assay Data
  • Calculated timeline durations for samples
  • NIH SAML Authentication
  • Folder & Role Permissions

Watch the HGRepo Presentation at LKUC 2020

At the 2020 LabKey User Conference,  Sandhya Xirasagar Ph.D., Lead, Clinical and Laboratory Informatics Section with NIAID and  Jason Barnett, Contract Lead, Medical Science and Computing, Inc. presented on the HGRepo Informatics Framework. Their presentation covers the informatics framework including the background and requirements for the scientific data management system, a demo of HGRepo and the future vision for the system. Watch below: