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BioToolKit is a collection of tools frequently used by bench biomedical scientists.
It is designed by bench scientists and easy to use. Functions include:
Standard PCR, reduces primer dimer and random primering. Batch mode.
Multipe PCR in one tube. Reduces dimers and random primering.
Degenerate primers based on single protein, or multiple alignments of proteins or nucleotides
Single pair of primers to amplify regions that are most diverse in a gene family
Multiple primer pairs, each uniquely amplify one gene in a family
Methylation-specific PCR primers
Design degenerate primers to profile large number of genes
Generates random primers for RAPD, AP-PCR, and RAP-PCR.
Design primers for optimizing gene expression
Primo Melt Primer design for DGGE or TGGT.
Primo PCR Primer Design
Abie Peptide Antibody Design
Abie Pro 3.0 designs antigenic peptide with reduced
background antibody cross-reactions. Proteomes of each species has a unique pattern of over-represented short amino acid sequences.
For example, GSGS is present in the mouse proteome for thousands of times and in thousands of proteins.
These over-represented sequences cause problems for peptide antibody design.
If present in a peptide used for raising an antibody, they may induce an antibody that cross-reacts with a large number of unwanted proteins.
By selecting a peptide with few over-represented sequences, a user will have a better success rate in raising an antibody with low background.
In addition Abie has a number of cool features.
Centrifugation speed/force conversion
Converts between relative centrifugation force (RCF, g) and centrifugation speed
(RPM, resolution per minute). To convert, select a rotor and then click on "<=>".
To save the parameters for a new rotor, type the rotor name in the rotor name field and click on save.
Molecular weight calculation for oligos, peptides, and chemicals
For chemicals, the composition should be in the following form: CaCl2 indicates
1 Ca and 2 Cl. (CHO)6 indicates 6 C, 6 H, and 6 O. If a composition is not recognized,
no calculation will be made. Note the element names are case-sensitive, i.e., a lower case
c will not be recognized as C or CL will not be recognized as Cl.
For DNA/RNA, degenerate codes are accepted. In the case of degenerate codes, the average
molecular weight will be calculated. For protein, the program reads sequences in
the single-letter codes.
Molar concentration calculator
This is a friendly calculator for calculations related to molar concentrations.
Spectrometer measurement for DNA and protein concentration
The parameters are preset for oligos and peptides. You may input your own parameters
for specific proteins, chemicals, or measurements using wavelengths other than UV.
Simply type in a new measurement type name, and fill in the parameters, and click on
Stock recipe calculator
Comes with recipes of tens of commonly used stock solutions. Input a total
volume, the program computes for you the amount of each ingredient needed.
Units conversion in 14 categories (length, volume, temperature, radioactivity, etc.).
Master cocktail mix calculator
For multiple reactions, one frequently makes a master mix of reagents and aliquot
to individual tubes or wells. Master mix calculator calculates the amount of reagents you need.
1. For time date conversion, the Gregorian Calendar is used. So it will not be
accurate for dates before the Gregorian Calendar is introduced.
2. Body Mass Index (BMI) = Weight (kg) / Height (m)2. The "normal" range is 20-25.
3. Body Surface Area (BSA) = 0.20247 x
Height(m)0.725 x Weight(kg)0.425.
GradeBook 1.02 provides the following functions:
1. Calculates final grades from exam and homework scores. Setup
allows varying weights for each score and discarding lowest scores.
2. Converts number scores to letter scores.
3. Save files in HTML format for display on the web or printing.
Setup allows hiding names and displaying partial student IDs.
Input label files should be Tab delimited text files with column
names in the first line. If you edit using Excel spreadsheet,
you could simply save it as a "tab-delimited" text file.
Column names must be unique.
To use the "Calculator", one of your column names must be
"overall", "overall score", or "overall grade". The final
calculated score will be saved in this column.
To convert to letter grades, check the "convert to letter grade"
checkbox, and a conversion table will appear below. You can
change the percentiles and their corresponding letter grades.
The Score Range will be calculated automatically from Percentile
and the Score Range will then be used to calculate the final letter
grade (since several students can have the same number grade, using
Percentile may randomly give some higher and others lower
3. HTML setup
You can select to display only a subset of columns in your
HTML page. If you need to display only partial student ID,
the id column must have the column name "ID", or "Student ID".
To print, open the HTML page with a web browser (e.g., Internet
Explorer or Netscape), and print the web page.
LabLabel 1.02 is a label printing software. In addition in printing
conventional address, stock, and package labels, it can add barcodes
to your labels. If your research is moving in the direction of
high through-put, bar-coding your reagents and data could result in
enormous savings in time and money.
Input label files should have either one of the following formats:
(1) Tab delimited text files with individual labels in separate
If you edit your label information in Excel spreadsheet,
you might want to save it as a "tab-delimited" text file. Each
label will be in one line and each field will then be printed in
a separated line. For example, the following stock label
5xTBA Date: 3/21/2002 By: Eric Heller
will be printed as
By: Eric Heller
(2) Text files with labels separated by blank lines:
The software will print the following in two labels:
Scale: 40 nmol
Scale: 40 nmol
To include barcodes, check the Barcode checkbox on the toolbar
menu. A randomly generated barcode will be included at the end
of each label if you don't specify where or the code string.
To insert barcode in the middle of a label, simply mark it with
the word "barcode".
Scale: 40 nmol
The above label will print a random barcode between "Sequence"
and "Date" lines. To add a specific barcode, include the barcode
string you want.
Scale: 40 nmol
Direction: reverse The above label will print a barcode encoded by the first 8
nucleotide sequence of the primer.
3. Barcode styles:
Code 39 and Code 128 are both alphanumeric barcodes of variable
lengths. They are often the choices for internal tracking.
Codebar is frequently used in blood banks. UPC is the industry
standard code for retail products.
Contact us if you need other styles.
For details, go to http://www.barcodehq.com/primer.html.
4. Label styles:
LabLabel 1.02 prints on 8.5x11 (A4) papers. Styles range from 80 labels
per sheet (4x20) to 1 label per sheet (1x1). These styles are
compatible with Avery label products. For details of supported
Avery products, go to
5. Preview will display the first page. Mouse-click will lead to
additional pages if available.
Microarray and High-Throughtput Data Analysis
MicroHelper 1.02 Merge datasets, check data integrity, filter noises, and normalize data.
Godlist Manager 1.0 Batch retrieve of gene information and sequences, and generate links to virtually all bioinformatics databases.
Heatmap Viewer 1.2 Heatmap, which uses a gradient of colors to represent data values, has been successfully used to present microarray data. The stand-only version of Heatmap Viewer 1.2 is designed to view any high throughput data including microarray data. The heatmap image can be saved as a JPEG file for including in other documents.
PrimerBase 1.2 PrimerBase is a small and practical database for storing, searching, and designing of oligo-nucleotides. Searches by keywords and by sequences.
PeptideBase 1.4 Similar to PrimerBase, this software allows users to store peptide information into a searchable database. Searches by keywords and by sequences.
BioDataFit 1.02: Data fitting for dose-response, ligand-binding, enzyme kinetics, and growth inhibition. EC50 calculation using four-parameter or sigmoidal model.
Chi-square: Chi-square test.
Correlation: Linear and non-linear correlation coefficients.
Probability: Poisson and Binomial probability distribution.
SVM Classifier: Train to classify multiple classes.
SVM SeqClassifier: Train to recognize sequence patterns.
Sample Size: Estimate sample sizes needed.
t-test: t-test calculator. Y
z-test: z-test, normal distribution calculator.
Suggestions and Bug Reports
Thanks for using BioToolKit 300. Please let us know if you feel
there can be additional improvements in the software. Send your
comments, suggestions, and bugs to email@example.com.
We will try our best to serve your needs in the next release of
Copyright © 2002-2004 Chang Bioscience Inc. All rights