Background: Problems with Files

Researchers and scientists often have to manage large numbers of files with a wide range of sizes and formats. Some of these files are relatively small, such as spreadsheets containing a few lines of data; others are huge, such as large binary files. Some have a generic format, such as tab-separated data tables; while others have instrument-specific, proprietary formats, such as Luminex assay files -- not to mention image-based data files, PowerPoint presentations, grant proposals, longitudinal study protocols, and so on.

Often these files are scattered across many different computers in a research team, making them difficult to locate, search over, and consolidate for analysis. Worse, researchers often share these files via email, which puts your data security at risk and can lead to further duplication and confusion.

Solution: LabKey Server File Repository

LabKey Server addresses these problems with a secure, web-accessible file repository, which serves both as a searchable storage place for files, and as a launching point for importing data into the database (for integration with other data, querying, and analysis).

In particular, the file repository provides:

• A storage, indexing and sharing location for unstructured data files like Word documents. The search indexer scans and pulls out words and phrases to enable finding files with specific content.
• A launching point for structured data files (like Excel files or instrument-generated files with a specific format), that can be imported into the LabKey Server database for more advanced analysis. For example, you can select files in the repository, and import them into assay designs or process the files through a script pipeline.
• A staging point for files that are opaque to the search indexer, such as biopsy image files.

Tutorial Steps

• Step 1: Set Up a File Repository
• Step 2: File Repository Administration
• Step 3: Search the Repository
• Step 4: Import Data from the Repository

First Step