2017 was a year of many milestones for the LabKey team. Our newest product, LabKey Biologics, launched in April and has been implemented at four leading pharma and biotech companies, we redesigned the LabKey Server user interface, and we took our compliance functionality to the next level with the introduction of compliant hosting and a suite of new features to support teams working within HIPAA, FISMA and CFR Part 11 compliant environments. LabKey is excited about what the next year has in-store and we want to share our vision for 2018 with the growing LabKey community.

Reinvesting Premium Dollars into Premium Functionality

Each year, LabKey invests in a number of development projects that premium subscribers have shared as key priorities. In 2018, we plan to dedicate development time to a variety of key areas including:

• Helping secure access to protected data with added support for PHI/PII handling
• Opening the power of R to more users in a secure manner by introducing sandboxing of R code execution
• Increasing the reliability and reproducibility of results via versioning of R engines and packages within RStudio configurations
• Streamlining data integration and enabling rich querying by adding support for clinical ontologies and controlled vocabularies
• Automating and expanding data acquisition options through pipeline file watchers and integration with cloud storage providers

Curious what new  functionality was introduced in 2017? Read our “What’s New” updates >

Delivering on the Biologics Roadmap

The LabKey Biologics team, in partnership with our product advisory council, has developed an aggressive roadmap for continued development of this flexible system for biologic discovery and development. In 2018, the team will be focusing much of their efforts on:

• Simplifying access to all relevant experiment data by enabling the grouping of samples, assay data, and notes by experiment
• Helping teams better understand their data by expanding reporting and visualization capabilities
• Making it easier for users to standardize and track the creation of media batches through usability improvements to the application’s media registration tools

Interested in learning more about LabKey Biologics? Watch our “Quick Look” video series >

Strengthening our Core Technology Infrastructure

In order to support our ongoing commitment to providing reliable software solutions, each year we dedicate resources to evolving our technology infrastructure to ensure its on-going stability. This year, we are largely focused on enhancements that will improve efficiency for both internal and external developers working with LabKey Server. Our key priorities include the development of a method for sharing JavaScript components between modules, fully supporting Java 9, and maintaining full compatibility with new versions of third-party components.

Refining the LabKey Server User Interface, According to User Feedback

We have heard from new users of LabKey Server that the current experience makes it difficult to get started using the platform. In order to make sure new users can be successful using LabKey Server from the get go, our UX team will be working with new users over the next few months to understand how we can improve our user interface and the tools we provide. In addition, we will be continuing to expand our our hosted solutions in 2018 to make it easier for organizations to adopt and support LabKey Server.

Want to learn more about the recent LabKey Server UI changes? Check out our “New LabKey Server UI” blog series >

In addition to strengthening our solutions this year, we want to continue to strengthen our relationships with you, the LabKey community. We hope that you will join us in this journey toward creating robust and powerful tools for accelerating research. A few ways that you can get involved this year include:

Providing Feedback on the New UI

As teams upgrade to LabKey Server version 17.3 and later, we encourage you to provide feedback about the new UI through the “Give Feedback” form that can be accessed in your LabKey Server account menu. This feedback is reviewed, prioritized, and used directly to help us make decisions about refinements to the LabKey Server UI.

Participating in a New User Walk-Through

Are you new to using LabKey Server? We want to hear about your experience and how we can improve! LabKey User Experience Manager, Jessi Murray, is looking for new users who would be willing to discuss their experience getting started with LabKey Server and how it could be improved.

Email Jessi Murray at jessim@labkey.com for more information!

Attending the LabKey User Conference

The LabKey User Conference is an opportunity for users to gather together and share about how they are using and extending the LabKey platform and solutions. Attendees also participate in round table discussions and work sessions with the LabKey developers where they can explore current challenges and shared feedback directly with the LabKey team.

Interested in speaking at the LabKey User Conference? Email conference manager, Kelsey Gibson at kelseyg@labkey.com for more information!

The upcoming redesign of the LabKey Server user interface includes a variety of updates; some of which are focused on look and feel, some on interface behavior, and some technical stability. All of these changes and enhancements were carefully selected because of the contribution they will make to the overall usability of the platform. Prior to the release of the new UI as part of LabKey Server v17.3, we wanted to give users a side-by-side look at some of the key updates and how they will differ from the current UI.[vc_row gap=”30″]

Landing Page

Many of the key changes to the LabKey Server UI can be seen upon your arrival on the LabKey Server landing pages. The new interface features an updated header style with a more compact navigation and reorganized menus, the addition of a new “frameless” webpart style, and updated logic that will hide the tab bar on home projects if there is only one tab present.[asvc_before_after before_image=”76688″ after_image=”76792″][vc_row gap=”30″]

Page Administration

In order to reduce the visual noise and present a cleaner UI for administrators, we have introduced a “page admin mode.” Options like “add web part” and tab editing will no longer be presented at all times and will instead only be visible when the user turns on page admin mode. Page admin mode can be easily turned on when edits to a page are needed and turned off when edits are complete.[asvc_before_after before_image=”76691″ after_image=”76793″][vc_row gap=”30″]

Data Grids

Several changes have been made to the LabKey data grids in order to declutter the grid navigation and increase readability. The most notable changes include the introduction of a more icon-driven button bar with tooltips for each action available on hover, a simplified “edit” link presentation, and the addition of row highlighting. [asvc_before_after before_image=”76684″ after_image=”76794″][vc_row gap=”30″]

Grid Customization

The customizing grids of data has been simplified in the new LabKey Server UI. With this update, filters and sorts added to a grid are always carried with view and no longer require an opt-in. Additionally, filters can be quickly edited using one click to reopen the filter pane or removed with by clicking the newly added [x] icon next to each filter definition.[asvc_before_after before_image=”76682″ after_image=”76795″][vc_row gap=”30″]

Menus

Updates to the LabKey Server menu are both visual and technical in nature. A major shift included as part of the redesign is the transition to menus written in Bootstrap instead of Ext, that take advantage of Bootstrap’s consistent styling and built-in behavior for multiple form factors. Sub-menu behavior has also been updated so that sub-menus now replace the menu content (with a back to menu option) instead of appearing next to the primary menu. This change makes the navigating to 2nd level sub menus a much cleaner experience, as users navigate within one menu frame instead of 3. Finally, type-to-filter functionality has been added to the menus with greater than 10 values. This can initially be seen in the “More Modules” list as well as the “Grid Views” list.[asvc_before_after before_image=”76697″ after_image=”76695″]

Related Resources

• Key Steps for a Successful UI Transition
• FAQs: LabKey Server Redesign
• LabKey Server Gets a Refresh
• Docs: New User Interface 

Whether you’re implementing a brand new software solution or updating an existing solution, changes that affect the workflow of team members are often a major pain point for organizations. Taking steps to manage and communicate these changes and their benefits to your users can greatly reduce the friction faced during implementation and, in turn, increase adoption by users. As you prepare to transition to the new LabKey Server UI (being released as part of LabKey Server v17.3), we encourage you to take the following steps to help manage this change and help make the UI transition a success.

Test the Redesigned Interface

Test the new interface extensively in your staging and/or test environments. As part of the 17.2 release of LabKey Server, we included the “Core UI Migration” experimental feature that allows administrators to turn on the new UI. While the interface is still in active development and certain elements may shift slightly, the bulk of the navigation changes are represented, and we encourage administrators to explore the new UI and test for:

Changes to your primary user workflows (editors, readers, administrators, etc.)
Go through the workflows of your primary users; click through the available buttons and navigate through the interface as your user would, checking for changes to their standard workflows.

Broken customizations
Check to see that customizations you have made to the interface are still functioning as expected. As part of the UI redesign, we have refactored a good portion of our own CSS in order to make it easier to maintain the platform in the long run. As a result customizations made to your server’s CSS may need updating.

UI bugs that should be reported to LabKey
Reporting bugs that you encounter during testing is an important part of the redesign process. Your feedback helps us identify and prioritize fixes that need to be made to the interface.

Identifying updates that need to be made to your server customizations and changes to your user workflows early will give you the opportunity to make adjustments and prepare for any new-interface training that might need to be done with users.

Set a Go Live Date

Decide on a date that you will make the transition to the new UI. Make sure you account for adequate time to test the new version, communicate upcoming changes and your transition plan, and train users on the new UI.

Communicate Upcoming Changes and Transition Plan

Communicating upcoming changes and their implications for your users early and often is crucial to a smooth interface transition. When communicating details about the interface transition to users, make sure to include information about:

• Transition timeline
• Key benefits of the transition
• Key changes/potential areas of frustration
• How users can ask questions
• How users can provide feedback

Provide User Training

Some of the changes being made to the LabKey Server interface during this redesign will affect how users perform certain tasks. If you discover through testing the interface in the context of your team’s key workflows that core tasks are affected by navigation changes, then providing training on how to accomplish this work in the new interface will help avoid frustration. For smaller changes, simply documenting the new process may be sufficient training, but in cases where a user’s workflow is significantly changed a training session may be more appropriate.

Answer Questions

Even with thorough testing, communication, and training, questions from your users are still inevitable. Develop and communicate how users can ask questions as they are are adjusting to the redesigned interface. Depending on the size of your team, that may mean communicating who the contact person is for questions, you may create a message board for questions and discussion, or you may host a handful of Q&A workshop sessions post-implementation. Whatever the method, making sure a user knows how they can have their questions answered will help prevent frustration when they encounter a change to their workflow.

Provide Feedback

Communicating feedback to the LabKey team is an essential part of the redesign process, and we are committed to making sure that you and your users have the best possible experience using LabKey Server. As you explore the redesigned interface in your test environment as an experimental feature, you can provide feedback using the “Give Feedback” button in the top right corner of the interface. You can also provide feedback directly to your LabKey account manager.

Related Resources

• FAQs: LabKey Server Redesign
• LabKey Server Gets a Refresh
• Docs: New User Interface 

LabKey partners at the Allen Institute for Cell Science are doing things a little differently. Launched in 2014 with a contribution from founder and philanthropist Paul G. Allen, the Institute was formed to integrate diverse technologies and approaches to study the cell as an integrated system. They are asking fundamental questions about cellular behavior to better understand healthy and pathological cells. Data and tools developed by the Institute are made publicly available to researchers around the world.

The Allen Institute for Cell Science team uses genome editing to add fluorescent markers to proteins in key cellular machinery and uses light microscopy to study the organization of that machinery and how it changes. During the generation of genome edited cell lines, they conduct quality control steps, including genotyping, stem cell marker analysis, karyotype testing, deep sequencing, and image-based assays. They also generate clonal lines for each gene and ensure that the cell line is useful for long term experiments. This work requires tracking cells, cell lines, genes, and all other quality control components through approximately 40 workflow steps.

The Allen Institute for Cell Science uses LabKey Server to capture metadata and assay data on each gene, cell, cell line, clone, and vector at each stage in the workflow: information that was previously housed in spreadsheets and raw data files. The Institute relies on the integrated views and query-ability of their LabKey managed data to efficiently identify target cells/cell lines to explore. Their use of LabKey Server also allows them to track the status of each entity as it makes its way through the processing pipeline, as well as monitor their complete workflow.

By centralizing their data, the Allen Institute for Cell Science will be able to accelerate their analysis and use insights gathered about their workflow to optimize their operations.

[vc_cta h2=”” shape=”square” style=”custom” custom_background=”#ededed”]Interested in using LabKey Server to optimize your workflow and accelerate data analysis?  Contact the LabKey team for more information![/vc_cta]

In support of the National Cancer Institute (NCI) and the Department of Energy (DoE) initiative to use large-scale computing to influence cancer science, NCI’s Surveillance, Epidemiology, and End Results (SEER) Program has partnered with LabKey to develop an abstraction workflow and Natural Language Processing (NLP) pipeline that will automate the annotation and review of free-text pathology reports.

The NCI SEER Program works to provide information on cancer statistics in an effort to reduce the burden of cancer among the U.S. Population. SEER currently collects and publishes cancer incidence and survival data from population-based cancer registries covering approximately 30 percent of the U.S. population. The registries receive at least one unstructured pathology report on the more than 450,000 cases reported annually that are used in conjunction with other sources to abstract relevant information on the cases.

The initial version of the application will allow SEER to identify and select pathology reports of interest using a Linguamatics-based text-mining tool and make them available in a LabKey Server portal for manual annotation and abstraction of key elements. An annotation and task management pipeline will manage the stages of the abstraction, annotation, and review process, ensuring consistency by standardizing tasks and automating the workflow. To ensure the security of data being processed and generated, the application will utilize LabKey Server’s role-based security model and facilities that ensure regulatory compliance.

Future phases of development will introduce the use of Natural Language Processing engines to further accelerate the annotation process. Manually abstracted data from the initial phase of the project will be used by DoE laboratories to help develop and train NLP algorithms that will then be used to automate the abstraction of large numbers of pathology reports.

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LabKey Server for Your Research

Interested in exploring LabKey Server as a bioinformatics solution for your organization? Contact us and the LabKey team will work with you to understand your needs and help determine if LabKey is the right fit for your research.

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