Single cell data management and analysis systems and methods

• US 10,616,219 B2
• Filed: 12/09/2015
• Issued: 04/07/2020
• 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
• Primary Examiner(s): Najjar, Saleh
• Assistant Examiner(s): Pan, Peiliang
• Application Number:
  US14/964,197
• Publication Number:
  US 20160170980A1
• Time in Patent Office: 1,581 Days
• Field of Search: 726 7
• 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 for integrating a scientific instrument with a remote computer system, the 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 network connection with a remote computer system;

transmitting the container data file to the remote computer system over the network connection;

receiving a command over the network connection from the remote computer system to acquire new scientific data under different acquisition parameters in response to an analysis by the remote computer system of the scientific data within the transmitted container data file;

controlling the scientific instrument in accordance with the received command to cause the scientific instrument to acquire the new scientific data using the different acquisition parameters;

transmitting, to the remote computer system over the network connection, the new scientific data; and

transmitting, to the remote computer system over the network connection, a protocol command causing the remote computer system to perform an analysis on the new scientific data, wherein the protocol command identifies a protocol template associated with the analysis to be performed by the remote computer system and wherein the protocol template is stored by the remote computer system, wherein the method is performed by a processor.

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

3. The method of claim 1 wherein the processor performs the method steps during an ongoing acquisition run such that the controlling step comprises the processor controlling the scientific instrument as it acquires the new scientific data.

4. The method of claim 3 wherein the processor performs the transmitting step in real-time as the scientific data is generated by the scientific instrument to stream the scientific data over the network connection to the remote computer system for the analysis.

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

6. The method of claim 5 further comprising:

the analysis server performing the analysis specified by the protocol command on the scientific data within the transmitted container data file; and

in response to the analysis, the analysis server sending the command for acquiring new scientific data under different acquisition parameters to the processor over the network connection.

7. 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.

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

9. The method of claim 8, 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.

10. 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.

11. 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.

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

13. The method of claim 11, 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.

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

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

16. The method of claim 1 wherein the analysis by the remote computer system indicates that the scientific data contained in the scientific data files is unsatisfactory.

17. The method of claim 1 further comprising:

the processor generating a graphical user interface configured to accept a selection of a modular template component specifying a portion of an experiment to be performed as part of the analysis, wherein the analysis comprises a plurality of modular template components, at least one of the plurality of modular template components being shared between the experiment and at least one other experiment; and

the processor receiving the selection of the modular template component and sending the selection with the container data file thereby causing the remote computer system to conduct the analysis on the scientific data contained in the container data file in accordance with the modular template component associated with the selection.

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

19. 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.

20. The method of claim 1 wherein the command comprises an instruction for using a new reagent to acquire the new scientific data.

21. The method of claim 1 wherein the command comprises an instruction for using a different instrument configuration for the scientific instrument to acquire the new scientific data.

22. The method of claim 21 wherein the different instrument configuration comprises at least one of an adjusted voltage of the scientific instrument and an adjusted compensation of the scientific instrument.

23. The method of claim 1 wherein the protocol template includes a constraint, and wherein the scientific data includes at least one value associated with the constraint.

24. The method of claim 1, further comprising creating a new container data file, wherein the new container data file comprises one or more new scientific data files representing the new scientific data, wherein the new scientific data are transmitted to the remote computer system over the network connection via the new container data file.

25. A computer program product for integrating a scientific instrument with a remote computer system, the 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 at least one processor to cause a computer to at least;

receive scientific data related to a biological sample from a scientific instrument,

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,

establish a network connection with a remote computer system,

transmit the container data file to the remote computer system over the network connection,

receive a command over the network connection from the remote computer system to acquire new scientific data under different acquisition parameters in response to an analysis by the remote computer system of the scientific data within the transmitted container data file,

control the scientific instrument in accordance with the received command to cause the scientific instrument to acquire the new scientific data using the different acquisition parameters,

transmit, to the remote computer system over the network connection, the new scientific data, and

transmit, to the remote computer system over the network connection, a protocol command causing the remote computer system to perform an analysis on the new scientific data, wherein the protocol command identifies a protocol template associated with the analysis to be performed by the remote computer system and wherein the protocol template is stored by the remote computer system, wherein the method is performed by a processor.

26. An apparatus for integrating a scientific instrument with a remote computer system, the 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,

wherein the interface is further configured to provide a protocol command over the network connection to the remote server to cause the remove server to perform an analysis on the scientific data transferred to the remote server, wherein the protocol command identifies a protocol template associated with the analysis to be performed by the remote server and wherein the protocol template is stored by the remote server.

27. The apparatus of claim 26 wherein the transferred operational data comprises a command from the remote server to acquire new scientific data under different acquisition parameters in response to an analysis by the remote server of the transferred scientific data;

and

wherein the interface is further configured to control the scientific instrument in accordance with the command to cause the scientific instrument to acquire the new scientific data using the different acquisition parameters.

28. The apparatus of claim 27 wherein the interface is further configured to transfer the scientific data to the remote server in real-time during an acquisition run by the scientific instrument.

29. The apparatus of claim 28 wherein the interface is further configured to (1) receive the command from the remote server during the acquisition run and (2) control the scientific instrument in accordance with the received command to cause the scientific instrument to acquire the new scientific data using the different acquisition parameters during the acquisition run as it is ongoing.