Labii electronic lab notebook (ELN) and laboratory information management system (LIMS)

Tuesday, August 27, 2019

ELISA Standard Curve with Labii ELN & LIMS in 3 steps

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ELISA (enzyme-linked immunosorbent assay) is a plate-based assay technique designed for detecting and quantifying substances such as peptides, proteins, antibodies and hormones. In an ELISA, an antigen must be immobilized on a solid surface and then complexed with an antibody that is linked to an enzyme. Detection is accomplished by assessing the conjugated enzyme activity via incubation with a substrate to produce a measurable product. The most crucial element of the detection strategy is a highly specific antibody-antigen interaction.

After an ELISA has been run, the data must be analyzed. The ELISA data analysis requires many different steps but it is still relatively simple compared to deep sequencing data analysis. The lack of market profit leads to limited solutions available. Excel and Graphpad are the two most used solutions.

The scatter chart is used to generate a standard curve in Excel. It usually takes around 15 steps to get the analysis results for one 96-well plate. Similarly, the scatter chart is also used when analyzing ELISA data with Graphpad. Before getting started with Graphpad, the data must be prepared and normalized in an excel sheet. The data can then copied to the GraphPad and use XY scatter chart.

Overall, the problem of the current methods are 1) they are tedious and requires 15-20 steps to finish the analysis to one 96-well plate; 2) easy to make mistakes - for all the manual steps involved, any single mistake involved by human will result in unspotted mistakes in the final results; 3) it is difficult to document the process - the data generated in biotech and pharmaceutical companies usually required to meet the regulatory requirements of FDA 21 CFR part 11. The manual steps make it very difficult to record all the processes.

To resolve such problem and make the data analysis of ELISA data more straightforward, Labii has developed a widget to perform the ELISA data analysis directly in the ELN platform. The widgets at Labii ELN & LIMS is a stand-alone function to edit or process a certain piece of data. We first create the layout of the 96-well plate for both layout and data, then we automatic all 15 steps at either Excel or Graphpad into one simple click. The widget can be inserted into experiments just like all other widgets. The detail documentation about the ELISA data analysis widget can be found here.

Here, I will show you how to perform ELISA data analysis with Labii ELN & LIMS in 3 steps:



Step 1: Prepare layout

Once you added the widget, you can prepare the ELISA layout by typing or import the data directly from your excel file. You can do so by dragging an excel file into the cloud area.

Prepare ELISA Layout
Prepare ELISA Layout


To enable the widget to recognize the data, please keep in mind:

  1. Use the first cell as the concentration unit. For example ug/ml.
  2. Use CONC to mark a serious of standard concentration in either the first column or first row.
  3. Use STD to mark a well as standard.
  4. Use BLANK to mark a well as blank.
  5. The same name is treated as duplicates. 
  6. Leave a well blank to exclude the data point in the analysis.
Please also follow these good practices to generate valid persuasive ELISA results:

  1. Run samples in replicate. To help evaluate the extent of error, each standard and sample should be tested in replicate (duplicate or triplicate, depending on the number of samples and room on the plate). Afterward, the average, standard deviation (SD), and coefficient of variation (CV) can be calculated to provide confidence in pipetting precision. As a best practice, the replicates should have a CV of less than 20%. If the CV is higher than 20%, consider the following (Reasons the CV may be high):
    1. Pipetting errors—Check pipetting technique. See the ELISA Troubleshooting Guide for proper pipetting techniques.
    2. Contamination of plates or reagents—Make sure plates and reagents are stored properly and don’t get cross-contaminated. Also, check reagents for expiration dates.
    3. Temperature across plate—Incubate plates in a stable environment to ensure even temperature.
    4. Evaporation—Use plate covers during all incubation steps.
  2. Run a standard curve on every plate. Every ELISA runs slightly differently depending on the operator, pipetting, incubations, and temperature. Taking these variables into account, it is a best practice to run a standard curve on each plate.
  3. Run a positive control sample. Running a control sample with a known concentration on each plate will indicate whether the ELISA was successfully executed. If the control sample represents the correct concentration, you can be confident in the results of the other unknown samples.
  4. Run blank samples. Blank samples are composed of the buffer or water with no protein sample included. These samples allow the subtraction of background absorbance from the rest of the data points to ensure the most accurate OD readings.
  5. Dilute samples so they fall within the linear range of the standard curve. To get the most accurate results, dilute the samples so they fall within the linear range of the standard curve. Values that fall toward the top or bottom of the curve tend to have a higher amount of error because of the assay’s limits. Many operators test samples at multiple dilutions to ensure that at least one of them falls within the linear range.
Step 2: Prepare data

Compare to data preparation in Excel and Graphpad, the data preparation in Labii is much simpler. Just drag the file over the cloud icon and all ELISA data will be load automatically.

Prepare ELISA Data
Prepare ELISA Data

Step 3: Perform the analysis

Once the data is ready, to perform the ELISA data analysis is as simple as a click. Click the Analysis button and the analysis will start right away. All results will be included in the analysis section once finished. The analysis only takes a few seconds.

Here are the details about the analysis:

1. Generate the average absorbance of blanks
Labii will use the layout you created at step 1 to find all blank wells. The average value will be calculated and displayed back to you.
Generate the average absorbance of blanks

2. Subtract background absorbance
The normalized value for all data points is calculated via subtracting the background absorbance (the average value of the blanks).  If the blank samples are reading higher than usual, this may indicate that there was an error in the assay.
Subtract background absorbance


3. Generate the average absorbance of the standard
If multiple standards are used, the absorbance of the standard at the same concentration will be calculated. This value will be used in plotting and fitting.

4. Fit the standard absorbance
On default, Labii uses linear regression to fit the standard absorbance with the standard concentrations. Labii also provide you the option to use other regression methods. You can click the edit icon to change the repression method:

  • linear - Fits the input data to a straight line with the equation y = mx + c. 
  • exponential - Fits the input data to an exponential curve with the equation y = ae^bx.
  • logarithmic - Fits the input data to a logarithmic curve with the equation y = a + b ln x.
  • power - Fits the input data to a power law curve with the equation y = ax^b. 
  • polynomial - Fits the input data to a polynomial curve with the equation anx^n ... + a1x + a0. 

Once it is finished, the fit equation will be generated and displayed for references. The calculated standard point will be used for plotting.
Fit the standard absorbance


5. Plot standard curve
A standard curve for the target protein by plotting the mean absorbance (y-axis) against the protein concentration (x-axis). A best-fit curve through the points in the graph will also be added based on the calculated value from fitting.
standard curve


6. Calculate SD, CV, and concentration
Concentration - The mean value of a sample/test/project will first generate. This mean value will then used in the fitting model to calculate the corresponding concentration. The final concentration will be multiple the dilution factor.
Standard Deviation (SD) - The standard deviation is a measure that is used to quantify the amount of variation or dispersion of a set of data values. The SD will be calculated for each sample.
Coefficient Variation (CV) - The coefficient variation (CV) is the ratio of the standard deviation σ to the mean µ: Cv=  σ / µ. This is expressed as a percentage of variance to the mean and indicates any inconsistencies and inaccuracies in the results. Larger variance indicates greater inconsistency and error. Labii calculates the CV values for each sample.
Once done, the sample, average value, SD, CV, and concentration will be displayed in a table. You can click the table header to sort the table.
Calculate SD, CV, and concentration


Summary

With Labii's ELISA Data Analysis widget, you can document and analyze the data in a few clicks, and the result is ready in a few seconds. Labii's ELISA Data Analysis widget is flexible and can meet all of your ELISA layout design. It also provides you multiple regression methods to meet your analysis for log files. Labii ELN & LIMS is the only ELN in the market that is able to provide this kind of applications. Please reach to us if you have any questions. Schedule a demo at http://schedule.labii.com.

Yonggan Wu

Thursday, August 22, 2019

3 Widgets to Manage Your Barcodes at Labii ELN & LIMS

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Biotech and pharmaceutical companies are continually seeking technologies to reduce costs and increase efficiency in data documentation and inventory management. Barcode systems have been around for quite some time but have seen a rise in use within the science field over the past 5 years. Barcodes now are widely used in medical/biotech/pharmaceutical labs because it helps them reduce costs by eliminating human error and also saves time when it comes to sample collection and tracking. Overall, the use of barcodes in labs will continue to grow as these companies see results that help streamline their lab processes and increase their ROI.

Barcode biotech


A barcode is a method of representing data in a visual, machine-readable form. Initially, barcodes represented data by varying the widths and spacings of parallel lines. These barcodes, now commonly referred to as linear or one-dimensional, can be scanned by special optical scanners called barcode readers.

Barcodes have evolved and now we see the QR code, similar to a barcode, is an example of an information matrix. QR codes are referred to as two-dimensional because they carry information both vertically and horizontally. Another direct result of this is the greater potential to carry information in a smaller space which is crucial for all biotech and pharmaceutical companies. QR codes have more error-tolerant compared to the barcode. Biosamples are usually stored in some hash conditions like liquid nitrogen (-196 C) or in a Freezer (-80 C). These conditions can easily damage the label or barcode, and the error-tolerant of QR codes makes it more and more common in inventory management.

Today, barcode systems are being used more than ever within the science field. Take that one step further as companies are now evaluating different LIMS vendors, with barcode functionality being a “must-have” feature. One of the key advantages of using a barcode system is reducing human error and usability (ease of use). On top of that, combine a LIMS platform like Labii ELN & LIMS and using barcodes, labs are much more efficient; quick and easy updates of samples, sample status, location, and more. Lastly, barcode systems allow labs to control their inventory by scanning in bulk as opposed to manually entering each and every item.

The time and money saved on with only a few advantages mentioned above is a key indicator of why barcode systems are here to stay and why it is crucial that LIMS providers include barcode functionality.

With the demand of barcode functionality rising throughout the market, Labii has responded by releasing 3 new widgets to manage barcodes within the LIMS platform to help achieve the goal of simplifying and streamlining how barcodes are being used today.

Label Widget

A label is a piece of paper, plastic film, cloth, metal, or other material affixed to a container or product, on which is written or printed information or symbols about the product or item. Labii enables you to design and print label(s) with the Label widget. Use this widget to print labels for samples/reagents, it’s best to work with the Barcode or QR code widget. Labii’s Label widget enables you to:

  • Customize what data to display. You have the flexibility to combine one or multiple fields for the label, and to hide or display the headers.
  • Use a commercial label size. Labii supports all available dymo label.
  • Customize the label size.
  • Customize the layout. The margin and font size can be changed directly.
Label Widget at Labii ELN & LIMS
Label Widget at Labii ELN & LIMS


Barcode Widget


The Barcode widget enables you to display the barcode for your interested value. Specifically:
  • You can decide what will be encoded in the barcode. On default, Labii UID is used. However, this widget allows you to keep your existing barcoding system and can encode your existing barcode values.
  • We also support all different types of barcodes. You can choose one from https://github.com/lindell/JsBarcode/wiki#barcodes
  • The layout of the barcode can be customized. Change the width and height of the barcode to make it fit perfectly for your labeling preferences.
  • The labels can also be customized. You have control on whether to include the labels or not, and what fields to include as the label, as well as the position of the label. 
Barcode Widget at Labii ELN & LIMS
Barcode Widget at Labii ELN & LIMS

QR Codes

Similar to Barcode widget, this QR code widget does everything the same, except it displays the QR code.  Here are the specifics:

  • You can decide what to be encoded in the QR code. On default, Labii UID is used. However, other columns can be selected as the QR code value.
  • We also support different QR Error correction level. The higher the level, the more complicated the QR code is going to be, and the higher the error tolerated. Learn more at https://www.qrcode.com/en/about/error_correction.html
  • The size of the barcode can be customized. Change the width to make it fit your labeling purpose.
  • The labels can also be customized. You have the call whether to include the labels or not and what fields to include as the label, the size for the label as well as the position of the label. 
QR Code widget at Labii ELN & LIMS
QR Code widget at Labii ELN & LIMS


Labii ELN & LIMS also supports scanning of QR codes. The scan function within Labii is extremely easy to use and can be done by using a mobile device as well. No additional scanner is required. To access the QR Code scan function, simply click the search icon from the navbar and select “SCAN.” Then scan the QR code and the results will be displayed in the search results! You can also use your traditional scanner on the search bar to scan the barcode/QR code created by Labii. For additional information on scan functions for Labii ELN & LIMS, view our dedicated support/tutorial page https://docs.labii.com/eln-and-lims/search#scan-qr-code.

Scan QR Code at Labii ELN & LIMS
Scan QR Code at Labii ELN & LIMS


Labii ELN & LIMS is at the forefront when it comes to keeping up with the evolution of ELN and LIMS platforms. The 3 new barcode widgets is another example of how Labii is leading the way and staying ahead of the market trends. If you’d like to learn more about Labii ELN & LIMS, feel free to schedule a free demo at http://schedule.labii.com.

Saturday, August 10, 2019

New sketch widget in Labii ELN & LIMS to write and draw

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Over the past 10 years, the adoption curve has changed dramatically as more and more people are shifting from using their desktop/laptop to using their smartphones/tablets for just about everything. Gone are the days of waiting to be at an office or home to use a desktop/laptop to browse the web, sending emails, finishing work-related tasks, and more.

The increase of tech within smartphones and tablets have made it to where people rely heavily on their mobile devices for work and that also changes how scientists and researchers document their lab notes. When it comes to documenting lab notes, scientists increasingly have the need to use their mobile devices to access their ELN platform and documenting their work. In today’s market, ELN vendors, for the most part, are lagging behind when it comes to adding features and functionality supporting the rise of mobile devices.

To help solve this problem, Labii has released a “Sketch” widget in their ELN & LIMS platform. The sketch widget enables scientists to capture and write down their ideas/notes, create different shapes and colors (perfect for tablet users with a stylus),  and edit images within their fingertips.

Sketch widget from Labii ELN & LIMS
Sketch widget from Labii ELN & LIMS


How to use the sketch widget in Labii ELN & LIMS


Here is an example of how to use the sketch widget:

  1. Go to tables on the navbar and select experiments
  2. Click the “+” icon to add “sketch widget”


Here are the tools/functionality within the sketch widget:
  • Save - save the sketch
  • Tool - drawing tools
    • Pencil - drawing pencil
    • Line - draw lines
    • Rectangle - create rectangles
    • Circle - create circles
    • Select - disables drawing and gives you the ability to modify existing elements in the canvas
    • Pan - disables drawing and gives you the ability to move the complete canvas at will which is useful to adjust the canvas when zooming in or out
  • Line width - change line width. Labii provides the options of 1px to 24 px.
  • Font color - change the font/line color
  • Fill color - change the fill color of a shape
  • Background color - change the curve background
  • Text - insert text into the canvas
  • Undo - undo the previous step
  • Clear - clear all data
  • Zoom in
  • Zoom out
  • Resize - resize the canvas
    • Default to 100% in width, 610px in height.
    • When width=100%, changing the screen size will change the shape of the drawing. To keep the shape of the drawing, use the resize function to save an absolute value of the width.
  • Image - insert a picture into the drawing
  • Download - download the drawing as a picture

Labii ELN & LIMS is truly designed for mobile and the sketch widget is one of many features that are perfect for users on the go. If you’d like to learn more about Labii ELN & LIMS, feel free to schedule a free demo at http://schedule.labii.com.

Thursday, August 1, 2019

Labii ELN & LIMS is nominated for the Outsell 300

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Outsell has released their Outsell 300 annual list where their analysts compile and rank the top emerging companies operating at the intersection of data, information & technology. These are the companies who are committed to innovations in the data, information, and analytics economy. The Outsell 300 program is part of a long-standing tradition each year and ensures that the world’s leaders in data, analytics, and information businesses grow revenue, mitigate risk, and execute better, in a fast-changing global market.

For over 20 years, Outsell has been the voice of the data and information industry. They combine unique data, industry-leading analytics, world-class events, and a thriving and growing peer-to-peer community to ensure their clients make the best possible decisions.

Labii ELN & LIMS is an online platform that has been built from the ground up to help scientists/researchers from biotech, pharmaceutical, and academic institutions to document, manage and interpret research data with our electronic lab notebook (ELN) and laboratory information management system (LIMS).

Scientists of various fields of study and research labs find it impossible to prescribe a single product for use in the company, campus, college, department or research group levels, because of the sheer diversity of interests, workflows, and preferences within the research community.

At Labii, we have worked directly with biotech/pharmaceutical companies and academic labs to develop a product that is customizable and extensible to meet the diverse needs of biotech, pharmaceutical companies, and academic labs. We modularized the type of data (notes, protocols, reagents, et.al) into tables, enabled custom columns for each table, and integrated stand-alone applications (widgets) to provide extensible features for ELN. Labii ELN & LIMS can be configured specifically for each organization to meet their specific needs in documenting, managing samples/inventories, track the operation of procedures (workflows), and more.

Learn more about the Labii ELN & LIMS at https://www.labii.com. Schedule a free demo with us at http://schedule.labii.com