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BioDiscovery does not support the use of proprietary file formats. Rather, BioDiscovery has adopted the use of tab delimited text files. Microsoft Excel files can easily be saved as tab delimited text files as outlined below. To save an Excel Doc as Tab Delimited Text:

  1. With the Excel document open, choose Save as… from the File Menu.
  2. Select Text (Tab Delimited) from the Save as Type Option at the bottom of the Save as Window.
  3. Specify a File name and location.
  4. Click Save.
  5. Microsoft will warn that certain elements cannot be saved in this format. Simply accept any warnings to complete the process.
  6. For additional information on the required text format, please see the documentation accompanying the software.

All BioDiscovery products are written in Java. Java can only see drive letters, not network locations. Therefore, the simplest solution is to map a network location to a drive letter. Under Windows, you can browse the network, right-click on the folder that contains the files and select Map Network Drive. Map it to a letter that is not being used by anything else (like “N” for Network or whatever you want). Then, when the BioDiscovery software asks for a file, simply select the N: drive and it will load the files across the network without transferring them locally first.

The  permissions are set up correctly by our software when you install it,  but only if you are using an account that has administrative privileges.  You can always un-install and re-install using an account that has  administrative privileges. If you need further assistance, please contact Support.

BioDiscovery software has been cited in hundreds of publications. Please use the full name of the software (e.g., Nexus Copy Number Discovery, NxClinical), the publisher (BioDiscovery, Inc.), and the URL when citing. The following are APA-style examples of how to cite BioDiscovery software:

BioDiscovery, Inc., Nexus Copy Number Discovery Version 9.0. El Segundo, CA: BioDiscovery, Inc. 

BioDiscovery, Inc., NxClinical Version 6.0. El Segundo, CA: BioDiscovery, Inc.

For a complete list of publications click here.

NxClinical Support

NxClinical is a platform-independent and comprehensive software solution for genetic data analysis, interpretation, management, and reporting for molecular genetics and cytogenomics labs.

Yes, multiple people can access the same data concurrently as all data is stored in a single central repository. Users can view the same sample at the same time from different locations, and when a user wants to make changes, the sample goes into edit mode and locks, preventing other users from making changes at the same time. Other users can continue viewing the data but cannot make changes. Once the first user has finished making changes, the changes are immediately visible to other users and another user can now edit the sample.

NxClinical is a comprehensive system which allows loading of raw probe-level data to segment and make calls and assists in interpretation of the results. The ability to visualize raw probe-level data along with calls and classification in a single software allows for immediate confirmation of events. The NxClinical software replaces multiple software systems performing different functions and streamlines the entire process from processing of raw data to generation of reports.

The data loaded into NxClinical is stored in a central database repository and can therefore be accessed from any location. The repository can be located within an institution’s network or on external cloud-based servers – the customer chooses where to house the data.

As NxClinical is an enterprise product we do not have a demo license as we do for the desktop product Nexus Copy Number. For more information on NxClinical and to get demo, please fill out the form here.

 

Algorithms are set; version changes indicate implementation of new features in the product Release Notes.

Unlimited; the only constraints are on the physical space and speed of the main server.

There are many public databases available including ClinGen/ClinVar, OMIM, DECIPHER, Imprinted Genes (Gene Imprint), Segmental Duplications (UCSC), and CIViC . Custom tracks you design and other public databases are available upon request.

The NxClinical Administrator at your site can add custom tracks to the visual display and table. Each user can configure this further to hide/show the available content.

Yes. The NxClinical Administrator at your site will need to set this up with assistance from BioDiscovery Support.

NxClinical is technology and platform agnostic. It handles both microarray and NGS data. Major manufacturers such as Illumina, Thermo Fisher (Affymetrix), Agilent, etc. are supported as well as custom platforms. You can load and analyze data from any manufacturer/platform in the same database.

BioDiscovery does not support the use of proprietary file formats. Rather, BioDiscovery has adopted the use of tab delimited text files. Microsoft Excel files can easily be saved as tab delimited text files as outlined below. To save an Excel Doc as Tab Delimited Text:

  1. With the Excel document open, choose Save as… from the File Menu.
  2. Select Text (Tab Delimited) from the Save as Type Option at the bottom of the Save as Window.
  3. Specify a File name and location.
  4. Click Save.
  5. Microsoft will warn that certain elements cannot be saved in this format. Simply accept any warnings to complete the process.
  6. For additional information on the required text format, please see the documentation accompanying the software.

If you would like to select events out for reporting, including the case’s ISCN report, here is a short tutorial that may help:

 

1. When opening a case for the first time, switch the sample’s view from “Admin Default” to “This Sample”. In doing so, you will save any event, filter setup and preference proper to this sample only. This is also under this view that you may lock your case.This sample - ISCN 2020

2. Click on the “Editing Mode” icon to enable any changes in events (size, call type, merging, deletion) and their selection for reporting. Then, in the Table, check the boxes that apply in the “Select” column.editing mode - ISCN 2020

3. Alternatively, you can also select your event under the “Event Details” view:event view - ISCN 2020

4. The ISCN report will now be displaying the selected event(s) only:ISCN 2020 report

5. If a case is normal, you may want to mark it as such. Click on the Sample’s Infoi ” icon and populate the “Affected Status” value. For “normal”, select “Unaffected”. Click on “Save Changes” to exit the Sample’s form.affected status - ISCN 2020

6. Exit the “Editing Mode”. Your preferences will be saved to this case.

7. If you are the final reviewers and signing off the case, you may want to Lock the case. Under the “This Sample” view, and Editing Mode off, click on the lock.locking the case - ISCN 2020

8. Back to the “Home” page, your case will now display two icons:

  • A lock indicating that the case has been reported out
  • A Text icon, allowing you to output the sample’s results, including the selected events only.return to home page - ISCN 2020

References to the User Manual:

Basic User Guide:

  • P18: EXPORTING A REPORT FROM QUERY RESULTS
  • p48: THIS SAMPLE
  • p78: LOCKING SAMPLES
  • pp91-96 SAMPLE REVIEW TABLE COLUMNS

Nexus Copy Number Support

Nexus Copy Number is a desktop software program for analysis of DNA copy number variation from aCGH, SNP array, and NGS data. In a user-friendly and efficient fashion, it allows users to detect the segments of DNA that have been lost or amplified and to detect allelic event changes (e.g. LOH). Sequence variants and gene expression results can also be loaded and analyzed alongside copy number variants.

Absolutely. Data from any number of different vendors (e.g. Illumina, Affymetrix, Agilent) and different technologies (e.g. aCGH/SNP microarray, WES, WGS) can be integrated, visualized, and analyzed together in Nexus Copy Number.

Nexus Copy Number supports virtually any aCGH, SNP array, or NGS platform, such as Affymetrix, Agilent, Illumina, custom arrays, Illumina HiSeq/MiSeq, Ion Torrent, Complete Genomics and more as well as data generated by various array image analysis software tools such as GenePix and ImaGene.

Copy number can be estimated (via BAM files) from whole-genome, whole-exome, and targeted NGS panels and associated sequence variants (typically via VCF and MAF files) can be visualized and analyzed. Nexus Copy Number also integrates single sample gene expression results to provide a complete genomics solution.

Yes, copy number can be estimated (via BAM files) from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted NGS panels in Nexus Copy Number software.

Yes, Nexus allows you to load sequence variants typically as VCF or MAF files. Custom files can also be loaded. Sequence variant data is uploaded via the Seq. Variation tab in the Load Data pop-up window. These variants can be viewed and analyzed alongside copy number variations.

 

Yes. Nexus Copy Number allows you to incorporate miRNA, mRNA, and RNASeq results on a per sample or cohort basis to identify genomic hot spots.

Yes. Nexus Copy Number allows you to incorporate external methylation data to identify genomic hot spots.

 

Data from virtually any organism can be used within Nexus. You just need to have the genome annotation files in the installation directory. The product comes only with human and mouse annotations but you can add any other organism. If your organism is not listed, we can generate the files for you.

The highest density arrays that are available on the market can be used. Nexus Copy Number can efficiently process the Illumina HumanOmni5-Quad arrays with 5 million probes or the Affymetrix CytoScan HD array with 2.6 million probes.

 

An  unlimited number of samples can be analyzed together. Some of our  customers have used several thousand very high-density arrays in a  single project on a typical desktop computer.

Preferred:
64-bit Platforms – Windows/OSX/Linux; Recommended: 4 GB RAM; Minimum: 2 GB RAM

Supported:
32-bit Platforms – Windows Win2k/WinXP/Win7; Recommended: 2.0 GHz or faster, 4 GB RAM; Minimum: 1.0 GHz Pentium, 2 GB RAM

You simply select files you want to load using the file chooser and then click on the Load Data button to load the data. In rare cases such as when loading dye-swap data or replicate data, you will create a Sample Descriptor (a tab de-limited text file) which will specify the sample types and files to load. Individual data type quick start guides (e.g. “Nexus Copy Number Quick Sheet for Affy CEL”, “Nexus Copy Number Quick Sheet for Illumina Using Plugin”) in PDF format are available in the docs folder of your Nexus installation folder. Please view the document specific for the type of data you are loading.

Nexus Copy Number offers the following algorithms for making segmentation calls.

  • Rank Segmentation: A robust variation of the well-known Circular Binary Segmentation (CBS) algorithm where the probe ranks are used to minimize the effect of outliers and drastically improve performance.
  • SNPRank Segmentation: An extension of the Rank Segmentation algorithm where B-Allele Frequency values are also included in the segmentation process generating both copy number and allelic event calls.
  • FASST2 Segmentation: A novel Hidden Markov Model (HMM) based approach that unlike other HMM methods does not aim to estimate the copy number state at each probe but uses many states to cover possibilities, such as mosaic events, and then make calls based on a second level threshold.
  • SNP-FASST2 Segmentation: An extension of the FASST2 algorithm but adding many more states to cover events related to the B-Allele Frequency values to make copy number and allelic event calls.

Yes. Nexus can quickly identify regions of genomic change that can distinguish between two populations (e.g. affected and unaffected individuals) and provide statistical confidence measure for each region.

The Nexus DB account request needs to be initiated from within the Nexus application. After launching Nexus, click on the “Login to Nexus DB” icon or click on “Nexus DB” in the menu bar and select “Login to Nexus DB.” In the resulting window, click on the blue “Register account” link (bottom left), fill in your information, and submit the form. You will receive your account username and password within two business days. Once you have your account, you can log into Nexus DB and query or browse the available projects. For further information on access, querying, uploading, downloading data to/from Nexus DB, please refer to the section on Nexus DB in the User Manual.

 

Yes. Nexus Copy Number allows you to bring copy number data that has already been segmented for further processing.

 

Yes. Some popular commercial oligo-array manufacturers supported by Nexus Copy Number include Affymetrix, Agilent, and Illumina.

 

In case of memory allocation issues with the BAM Multiscale Reference Builder utility while creating the reference file for the BAM (multiscale reference) data type:

It is recommended to increase the memory allocated to the Multiscale BAM Reference Builder to about 50% of total memory available; at minimum the reference builder requires 4GB of memory.

For PCs:
Edit the “MultiScale BAM Reference Builder.lax” file in the installation directory. E.g. for win64 machines, to increase the memory to 8GB, edit the -Xmx parameter in the following line to 8000m:

lax.nl.java.option.additional=-Xms500m -Xmx8000m

For MACs:
Edit the .plist file for the MultiScale BAM Reference Builder application to increase memory allocation to about 50% of total memory. E.g. if you have 16GB memory, change the -Xmx value to 8000m. e.g. from

<string>-Xmx4000m<string>

to

<string>-Xmx8000m<string>

For all other memory issues, follow the instructions below.

For 64-bit PCs:
Try increasing the space allocation by editing the file C:\Program Files\BioDiscovery\Nexus 9\nexus 9.lax increasing the parameter -Xmx in the line below. If you have 8gig of RAM, then change the Xmx parameter to 4000m (4g), about half the RAM on your computer. E.g. from

lax.nl.java.option.additional=-XX:-UseGCOverheadLimit -Xms500m -Xmx2200m -Dnl_floating=undefined -Dnolock=true

to

lax.nl.java.option.additional=-XX:-UseGCOverheadLimit -Xms500m –Xmx4g -Dnl_floating=undefined -Dnolock=true

For MACS:
Please go to /Applications/BioDiscovery/Nexus 9 and ctrl-click on Nexus 9.app and select the option “Show Package Contents.” Open the Contents folder and open info.plist with TextEdit to increase the memory allocation to about 75% of the total RAM on your computer.

For example if you have 8 gigs of RAM then change the –Xmx parameter between array tags (line depicted in bold) from

<array>
<string>-Xms32M<string>
<string>-Xmx64M<string>
<string>-Xms500m<string>
<string>-Xmx2500m<string>

To

<array>
<string>-Xms32M<string>
<string>-Xmx64M<string>
<string>-Xms500m<string>
<string>-Xmx6g<string>

Save the file and restart Nexus Copy Number. This increases memory allocation to 6gigs.

For 32-bit PCs:
Please go to the folder C:\Program Files\BioDiscovery\Nexus 9.0\ and edit the file Nexus 9.0.lax in Notepad, and change the -Xmx value in the following line from

lax.nl.java.option.additional=-XX:-UseGCOverheadLimit -Xms500m –Xmx800m -Dnl_floating=undefined -Dnolock=true

to

lax.nl.java.option.additional=-XX:-UseGCOverheadLimit -Xms500m –Xmx1100m -Dnl_floating=undefined -Dnolock=true

Save the file and restart Nexus Copy Number. This increases memory allocation to 1100 mbs which is a max for 32-bit computers.

For 32-bit PCs that show error message “Cannot start Java virtual machine”:

Please go to the folder C:\Program Files\BioDiscovery\Nexus 9.0\ and edit the file Nexus 9.0.lax in Notepad, and change the line:

lax.nl.java.option.additional=-XX:-UseGCOverheadLimit -Xms500m –Xmx1200m -Dnl_floating=undefined -Dnolock=true

to

lax.nl.java.option.additional=-XX:-UseGCOverheadLimit -Xms500m –Xmx1000m -Dnl_floating=undefined -Dnolock=true

Save the file and restart Nexus Copy Number. This decreases memory allocation to 1000 mbs which will allow java to start up.

 

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