Life Technologies Corporation

Thomas Wessel

Xin Mathers

Jacob K Freudenthal

Jeffrey A Marks

Nivedita Sumi Majumdar

Francis T Cheng

David C Woo

Yong Chu

Marcin Sikora

Harrison Leong

David Hoard

Hon Siu Shin

Gordon A Janaway

Thomas B Morrison

Manjula Aliminati

Levente Egry

Shakila Pothini

Jamie Cho

Pratik Simon Soares

Shweta Raizada

Salil Kumar

Joanna Lankester

Daniel Wessel

Christopher Fong

Kok Siong Teo

Michael Uy

Zeng Wei Chu

Lik Seng Lau

Zeqi Tan

Chin Yong Koo

Way Xuang Lee

Eric Van Helen

Howard Weiss

Lian Seng Loh

David Woo

Soo Yong Lau

Wei Fuh Teo

Kuan Moon Boo

Mingsong Chen

Tiong Han Toh

Mauro Aguanno

Huei Steven Yeo

A method for determining false positives calls in a biological data plot is provided. The method includes identifying a first data cluster as non-amplification data points within the biological data plot and identifying a second data cluster as wild-type positives within the biological data plot. The method further includes estimating a position in the biological data plot of a center of the first and second data clusters. The method further includes determining, for each data point within the first data cluster, a probability of belonging to the first data cluster and determining, for each data point within the second data cluster, a probability of belonging to the second data cluster. The method includes applying a probability threshold for each data point within the first and second data cluster to identify false positives.

Determining the limit of detection of rare targets using digital PCR

A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.

Methods and systems for a digital PCR experiment designer

A system for analyzing biological data, comprising: a storage configured to store a plurality of data files containing biological data obtained from a plurality of devices; a server configured to: host a plurality of applications, each configured to be implemented on the server and to provide analysis, manipulation, comparison, visualization, or a combination thereof, of the biological data included in the data files, wherein the plurality of applications allow a user to analyze different data files related to the same sample and compare the results of the analysis.

Methods and systems for knowledge discovery using biological data

In one exemplary embodiment, a method for validating an instrument is provided. The method includes receiving amplification data from a validation plate to generate a plurality of amplification curves. The validation plate includes a sample of a first quantity and a second quantity, and each amplification curve includes an exponential region. The method further includes determining a set of fluorescence thresholds based on the exponential regions of the plurality of amplification curves and determining, for each fluorescence threshold of the set, a first set of cycle threshold (C) values of amplification curves generated from the samples of the first quantity and a second set of Cvalues of amplification curves generated from the samples of the second quantity. The method includes calculating if the first and second quantities are sufficiently distinguishable based on Cvalues at each of the plurality of fluorescence thresholds.

Methods and systems for instrument validation

A method for calibrating a biological instrument is provided. The method comprises the steps of acquiring an image of at least one biological sample array, determining a first region of interest within the image, wherein the first region of interest comprises a first plurality of locations on the at least one biological array; and identifying within the first region of interest, a plurality of image elements associated with each of the first plurality of locations on the at least one biological array.

Methods and systems for streamlining optical calibration

In one exemplary embodiment, a method for calibrating an instrument is provided. The instrument includes an optical system capable of imaging florescence emission from a plurality of reaction sites. The method includes performing a region-of-interest (ROI) calibration to determine reaction site positions in an image. The method further includes performing a pure dye calibration to determine the contribution of a fluorescent dye used in each reaction site by comparing a raw spectrum of the fluorescent dye to a pure spectrum calibration data of the fluorescent dye. The method further includes performing an instrument normalization calibration to determine a filter normalization factor. The method includes performing an RNase P validation to validate the instrument is capable of distinguishing between two different quantities of sample.

Methods and systems for biological instrument calibration

A method for improving image quality is provided. The method includes receiving image data of a substrate, wherein the image data is generated by imaging the substrate, and an image is generated from the image data. The method further includes generating a background representation from a background noise portion of the image, wherein the background portion includes signal information undesired for further processing and generating a background subtracted image by subtracting the background representation from the image. In this way, a separate background image is not needed to subtract the background from the image including the regions-of-interest to improve image quality.

Methods and systems for background subtraction in an image

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Pleasanton, CA, United States of America

Thomas Wessel