Category: Products & Services

31 Jan 2018

Two Key Things Your Spreadsheet-Based Research Data Management Strategy is Lacking

High-throughput analysis techniques are incredibly powerful and provide teams with more data than ever. While that depth of data often holds the key to scientific insights, organizing such large quantities of data in a consistent and discoverable way has become a major challenge for research teams.

Many teams rely on spreadsheet-based systems to organize and manage their data. This approach becomes less-effective as research scales because spreadsheet-based strategies lack two essential characteristics:

1. Consistency

Spreadsheet data management lacks consistencyManual file management relies on the individual contributor’s abilities to consistently create, name, and store data files. This opens the door to a wide range of human errors that will ultimately impact the discoverability and reliability of your data. Common consistency errors that result from manual data management include:

  • Poorly named files
  • Inconsistent locations
  • Duplicate files

2. Discoverability

Spreadsheet data management lacks discoverabilityCollecting data is a giant hurdle in research, but in reality, it is just the first of many. Researchers need to be able to locate datasets of interest in order to conduct analysis. In a file based environment, discoverability of files is dependent on the consistency with which they are maintained. Were they saved in the correct location? Have they been named according to an agreed upon convention? Is there a clear authoritative file or are there duplicates?

A hitch in any one of these areas can severely hinder the discoverability of your data and make it significantly more difficult to:

  • Track what research data has already been collected
  • Find the data you are looking for when it comes time to analyze

Biology-Aware Data Management with LabKey Server

Scientific data management systems like LabKey Server, help increase the consistency and discoverability of your research data. LabKey Server increases the consistency of data management by providing structured data grids for storing various type of research data. Each data grid type also captures relevant metadata, specific to that data type, in order to help make data more discoverable.

Research-Centric Data Structures

Unlike spreadsheets that treat all types of data the same, LabKey Server provides four primary data structures with unique features to better support common types of research data.*

LabKey Assays – Assay data grids capture data generated from individual experiment runs. Assay data is automatically structured in a batch-run-results hierarchy when data files are added. LabKey Server supports data a variety of common assay designs out of the box, but teams can also design their own assay data structure using LabKey’s General Purpose Assay Design.

LabKey Datasets – Datasets track patient/subject measurements over time. LabKey datasets are automatically aligned and joined together, making it easy to query the integrated data and to create visualizations from multiple datasets.

LabKey Specimens – Specimen repositories track the status of each specimen and vial in your inventory. Built-in reports provide a birds-eye view of specimen information, and advanced search capabilities allow for easy location of specimens.

LabKey Lists – LabKey lists provide general purpose, online, interactive grids for any tabular data. Data stored as a LabKey list can be sorted, filtered, and visualized using built-in tools.

Storing data in a consistent, structured manner is the key for teams that hope to achieve maximum efficiency in operations and maximum value from their data. Not only is it much simpler to find data when it is stored in an expected location, but the centralization and integration makes it possible to query data to more quickly locate information of interest.

Interested in learning more about how LabKey Server can increase consistency and discoverability of your research? Contact the LabKey team for more information or request a demo!

*To learn how to add data to LabKey Server, read documentation >

18 Jan 2018
LabKey Vision 2018

LabKey Vision 2018

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.

LabKey Server Premium Functionality: R Studio, PHI/PII Handling, Clinical Ontologies

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 >

Biologics R&D Roadmap: Experiment Grouping of Samples, Assay Data, Lineage 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 >

LabKey Software Infrustructure: Java 9, Javascript Shared ComponentsStrengthening 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.

LabKey Server UX Refinements: New User Experience, Hosted Data Management Solutions, Compliant HostingRefining 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!

20 Dec 2017

LabKey Biologics: A Year in Review

As this year comes to a close, we wanted to take a few minutes to reflect on the year and thank you for joining us on the LabKey Biologics journey. It has been an amazing year and we couldn’t be more excited about what’s coming in 2018!

Launching LabKey Biologics

One of the key parts of developing this application has been the engagement from our LabKey Biologics Product Advisory Council. Since its inception, we’ve been meeting monthly with eight different biotech, pharma, and academic institutions to get feedback. They’ve let us know what we’re doing right (and wrong) and have been invaluable in guiding the product development.

After working with the Product Advisory Council and our initial collaborator, Just Biotherapeutics, for 18 months, we officially launched LabKey Biologics in March. This first version focused on:

Just Biotherapeutics has been rolling out LabKey Biologics and has registered hundreds of biological entities, used workflow management to request thousands of assays, and uploaded analytical data for tens of thousands of samples. Several other members of our advisory board have also become clients and are in the process of implementing LabKey Biologics at their organizations.

Following the release of LabKey Biologics, we had the chance to talk with hundreds of individuals about the new product at PEGS Boston and Bio-IT (we’ll be at both shows again in 2018). Gathering feedback from folks in different roles throughout the industry, active users, and advisory board members has helped us improve the product and plan for future enhancements.

Since we launched in March, we’ve worked on many different improvements to the product. Some of the larger efforts include:

  • Additional Methods to Upload Assay Data
  • Defining the Lineage of a Sample, from Bioreactor Run to Purified Antibody
  • Media Registration – More Options and Ease of Use
  • Updates to the User Interface

What’s Next

As we look to 2018, we are excited to continue expanding the functionality of LabKey Biologics. We’ve got big plans for the next 12 months, including:

  • Defining Experiments
  • Building Analyses and Reports
  • Mapping and Characterizing Post-Translational Modifications
  • Improvements to Bulk Import of Entity Registry, Assay, and Media Data
  • Integrating Custom Assay Definitions with LabKey Biologics

Product Feedback

We’re always interested in feedback! We’d love to connect with each of you in the new year, and have a conversation (or several) to hear about your needs and thoughts on the product’s direction. If you’d like to learn more about LabKey Biologics, we’re hosting a free Intro to Biologics webinar on January 9.

Don’t hesitate to get in touch with us – and best wishes to you in the New Year!

LabKey Biologics Team

Ryan Luce, Product Manager
Email: ryanl@labkey.com

Kevin Krouse, Lead Software Engineer
Email: kevink@labkey.com

21 Nov 2017

What’s New in LabKey Server v17.3

We are excited to announce the release of LabKey Server v17.3! This release marks the launch of our newly redesigned user interface and includes a wide variety of other key feature and security enhancements.

Feature Highlights of Version 17.3

User Interface Update

The 17.3 release includes big improvements to the LabKey Server user interface. Enhancements include:

  • Project Navigation – Project and folder navigation has been redesigned as a single-column scrollable list, which also works well on tablets and other small windows. (docs)
  • Frameless Web Parts – You now have the option to render cleaner looking pages using “frameless” web parts, which removes the web part title, the surrounding border, and the top banner. (docs)
  • Grid Interface – Improvements include: (1) new graphics and buttons, (2) filters and sorts are automatically included when saving a custom view, and (3) when saved views exceed 10 items, a text-based filtering box makes it easier to locate the relevant views. (docs)

Electronic Signatures
Electronically sign a data grid snapshot, and specify a reason for signing. Signed documents and associated metadata, such as the signatory, the date of signing, etc. are extensively logged for auditing purposes. (docs)

REDCap Improvements
REDCap integration has been updated and enhanced, including a new graphical user interface which replaces the XML-based configuration interface, making it easier to configure connections and data export from REDCap servers. (docs)

For details on all the new features, read the release notes on the LabKey Support Portal, or download the latest version of LabKey Server.

19 Sep 2017

Before & After: A Side-by-Side Look at the New LabKey Server UI

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.

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.

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.

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.

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.

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.

12 Sep 2017

Key Steps for a Successful UI Transition

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

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.

01 Aug 2017

FAQs: LabKey Server Redesign

In the 17.2 release of LabKey Server, we included an experimental feature that allows teams to explore the beta version of the redesigned LabKey Server UI (scheduled for full release as part of v17.3). The key priorities for this redesign are to transition the platform to using modern technologies that will increase its stability and ease of use, and to respond to user feedback about areas of the platform that needed to be reworked to better support today’s users.

As you explore the new UI, we encourage you to provide feedback about the design and any technical bugs you come across. This will help us make adjustments during the next few months of active development before the initial release. Below are the answers to some common questions you may have when testing the new UI on your LabKey Server. We will continue to add to this list as we receive additional feedback.

Do we have to transition to the new interface or can I keep using the old one?

In 17.2, you’ll have the option to turn on the new look and feel by going to the experimental features listed under the Admin Console and enabling “Core UI Migration.” This will be opt-in, but we recommend you take a look now and provide feedback!

Since this turns the new interface on for all users, and this is still undergoing significant development, we recommend that you turn this on first on your test and/or staging server(s) and not yet on production.

With the 17.3 release, all installs will be moved to the new interface and the old UI will no longer be available for use.

What will happen to my custom CSS when we switch to the new UI?

To support the redesigned UI we are utilizing the standard Bootstrap framework and refactoring a good portion of our own CSS in order to make it easier to maintain the platform in the long run. It is likely that your custom CSS will need updating as a result of these changes.

We recommend that you move your staging server over to the new UI as soon as possible in order to evaluate and update any custom CSS that does not render correctly in the interface. If you are a Premium Edition client, contact your LabKey account manager if you need support making these changes.

Why does my site logo look broken?

By default, the 17.2 release uses the Seattle theme, which has a dark blue bar at the top of the header. Logos that use transparency may look wrong if they were previously on a white background. To fix this, you either upload an alternate version of your logo that will render well on dark background or you can switch to the Seattle Light theme which has a white top bar by going to Admin Console and adjusting your Look and Feel Settings.

Can I change the colors used in the interface?

In the beta release of the interface with v17.2, there are two default theme options to choose from: Seattle and Seattle Light. With 17.3, we expect to have the full suite of themes available for use, with a light and dark version of each. Additionally, you will still have the option of writing custom CSS.

We plan to introduce additional customization options as part of future releases that will allow you to more easily change change specific variables without writing your own CSS.

How do I add webparts to my pages in the new UI?

In order to streamline our page controls, we decided to make those that are used less often only show up conditionally. Most of our administrative controls are now available only when you go into admin editing mode. To turn this on, you can go to the admin dropdown and select “Page Admin Mode” (provided you have administrator permissions):

LabKey Server Page Admin ModeWhile this editing mode is on, you have the ability to add, move, or remove webparts and adjust page tabs just as you did in the previous versions. You can exit this mode by clicking on “Exit admin mode” in the header or in the admin dropdown.

LabKey Server Exit Admin Mode

I found a bug with the new UI. How do I report it?

You can report bugs using the “Give Feedback” link in the top right corner of the new UI. This link will redirect you to a feedback form on the LabKey Support Portal where you can report issues as well as general feedback. Please provide clear steps on how to reproduce bugs you encounter so that we can appropriately investigate and prioritize changes to be implemented in the 17.3 release and beyond.

I use ExtJS 4.x in my applications, why does my view not show up in the new UI?

With the introduction of the new UI we were able to move away from ExtJS 4.x for rendering menus. This was the last “site-wide” dependency we had on ExtJS, however, we still continue to use it throughout the product in different views, reports, and dialogs. To manage these usages we use our dependency framework to ensure the correct resources are on the page. The framework provides a variety of mechanisms for module-based views, JavaServer Pages, and Java.

If your applications do not declare their dependencies, it is likely they will fail to load when they are loaded independently (without other views/apps on the page that might be declare the same dependencies).

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.

14 Jul 2017

What’s New in LabKey Server v17.2

We are excited to announce the release of LabKey Server v17.2! This release includes valuable enhancements to platform features and performance improvements including:

For a complete list of updates and enhancements included in LabKey Server v17.2, check out the release notes.

Download LabKey Server v17.2 >

*Premium feature, please contact your LabKey account manager for additional information and configuration support.

LabKey Server Gets a Refresh

Also included in the LabKey Server v17.2 release is an experimental feature allowing administrators to explore the beta version of the redesigned LabKey Server user interface (scheduled for full release November 2017). We encourage administrators to explore the in-development UI in their dev/test environments and provide feedback prior to the full release.

Learn more about the UI refresh >

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