Single Cell Data Management and Analysis Systems and Methods

• US 20160170980A1
• Filed: 12/09/2015
• Published: 06/16/2016
• Est. Priority Date: 12/11/2014
• Status: Active Grant

• Current Assignee: FlowJo, LLC (Becton, Dickinson & Co)
• Original Assignee: FlowJo, LLC (Becton, Dickinson & Co)
• Inventors: Stadnisky, Michael D., Almarode, Jay
• Granted Patent: US 10,616,219 B2
• Time in Patent Office: Days
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• CPC Class Codes: G16B 50/20 Heterogeneous data integration
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: H04L 63/0876 based on the identity of the terminal or configuration, e.g. MAC address, hardware or software configuration or device fingerprint
• CPC Class Codes: H04L 67/06 specially adapted for file transfer, e.g. file transfer protocol [FTP]
• CPC Class Codes: H04L 67/12 specially adapted for proprietary or special-purpose networking environments, e.g. medical networks, sensor networks, networks in vehicles or remote metering networks
• CPC Class Codes: H04L 69/04 Protocols for data compression, e.g. ROHC

Abstract

Disclosed herein are a number of example embodiments for data management and analysis in connection with life science operations such as flow cytometry. For example, disclosed herein are (1) a networked link between an acquisition computer and a computer performing analysis on the acquired data, (2) modular experiment templates that can be divided into individual components for future use in multiple experiments, and (3) an automated pipeline of experiment elements.

Claims

1. A method comprising

receiving scientific data related to a biological sample from a scientific instrument;

creating a container data file, wherein the container data file comprises one or more scientific data files representing the received scientific data and a manifest data file listing the one or more scientific data files contained within the container data file;

establishing a connection with a remote computer system;

transmitting the container data file to the remote computer system over the connection,

wherein the method steps are performed by a processor.

2. The method of claim 1 wherein the scientific instrument is a flow cytometer.

3. The method of claim 1 further comprising:

the processor sending commands to the scientific instrument to control the scientific instrument as it acquires the scientific data; and

the processor generating the scientific data files in response to the received scientific data from the controlled scientific instrument.

4. The method of claim 1 wherein the remote computer system is an analysis server configured to analyze the scientific data contained within the container file.

5. The method of claim 4, further comprising:

the processor communicating a command to the analysis server, the command configured to select an analysis protocol stored on the analysis server for execution thereby with respect to the scientific data contained within the container file.

6. The method of claim 1 further comprising the processor compressing the scientific data files before creating the container data file, and wherein the container data file comprises compressed versions of the scientific data files.

7. The method of claim 6 wherein the container data file further comprises metadata indicating parameters and conditions of the scientific instrument while the scientific instrument acquired the scientific data.

8. The method of claim 7, wherein the metadata further indicates at least one member of the group consisting of scientific instrument type, patient identification data, a reagent used during data acquisition, user-submitted annotations, and a digital signature.

9. The method of claim 1 further comprising the processor calculating checksum values for each scientific data file contained within the container data file, and wherein the manifest data file lists the calculated checksum values associated with each scientific data file.

10. The method of claim 1 wherein the connection is a secure connection, and wherein the establishing step comprises the processor:

pinging the remote computer system through an unsecure uniform resource locator (URL);

exchanging authentication credentials with the remote computer system to gain access to a secured URL; and

switching to the secure URL at the direction of the remote computer system when the remote computer system authorizes the processor based on the exchanged credentials.

11. The method of claim 10, wherein the authentication credentials comprise a MAC address associated with the processor.

12. The method of claim 1 further comprising the processor monitoring a watch folder file directory where the scientific data files are stored;

and

detecting a predetermined data file indicating that the scientific instrument has finished acquiring scientific data; and

creating the container data file and establishing the secure connection after the processor detects the predetermined data file.

13. The method of claim 12, wherein the processor automatically creates the container data file and uploads the container document upon detection of the predetermined data file.

14. The method of claim 13 wherein the predetermined data file comprises the manifest data file.

15. The method of claim 1 further comprising:

the processor receiving a command from the remote computer system to acquire the scientific data under different acquisition parameters in response to the remote computer system finding the scientific data contained in the scientific data files unsatisfactory.

16. The method of claim 1 further comprising:

the processor generating a graphical user interface configured to accept a user'"'"'s selection of a modular template component specifying a portion of an experiment to performed as part of the experimental analysis or a protocol comprising a plurality of modular template components;

the processor receiving a user'"'"'s selection of a modular template component specifying a portion of an experiment to performed as part of the experimental analysis or a protocol comprising a plurality of modular template components;

sending the user'"'"'s selection with the container data file thereby causing the remote computer system to conduct data analysis on the scientific data contained in the container data file.

17. The method of claim 1 wherein the container data file is an archival cytometry standard (ACS) file.

18. The method of claim 1 wherein the processor is resident on a member of the group consisting of (1) an acquisition computer associated with the scientific instrument, and (2) the scientific instrument.

19. A computer program product comprising:

a plurality of processor-executable instructions that are resident on a non-transitory computer-readable storage medium, wherein the instructions are configured for execution by the processor to cause the computer to (1) receive scientific data related to a biological sample from a scientific instrument;

(2) create a container data file, wherein the container data file comprises one or more scientific data files representing the received scientific data and a manifest data file listing the one or more scientific data files contained within the container data file;

(3) establish a connection with a remote computer system; and

(4) transmit the container data file to the remote computer system over the connection.

20. An apparatus comprising:

a processor configured to execute an interface, the interface configured to bi-directionally link a scientific instrument with a remote server to (1) transfer scientific data acquired by the scientific instrument over a network connection to the remote server, and (2) transfer operational data for controlling an operation of the scientific instrument from the remote server over the network connection to the scientific instrument.