Arxspan BioDrive: A Versatile Solution for Molecular Biology

insights from industryAdrienne Lemieux
Ying Zhao
Daniel James

What is SciY, and how does it aim to transform lab and manufacturing ecosystems?

SciY is composed of four different companies unified by a common vision. Firstly, we have Arxspan, a fully integrated cloud platform designed for the management of scientific data. This platform seamlessly merges chemistry and biology data within a unified system.

Next, we have Mestrelab Research, which provides analytical data processing, analysis, visualization, and reporting, along with analytical workflow automation through its Mgears application. It also specializes in connecting software to instruments.

Moving on, there is Zontal, a GXP-compliant cloud platform for integrated digital labs with life sciences analytics and long-term data preservation capabilities. Finally, we have Optimal, which offers PAT software solutions for real-time process control, along with customized automation, machinery, and integration services.

With SciY, we have established a unique ecosystem of vendors that seamlessly integrate through fair data platforms, enabling digital transformation for a wide range of laboratory and manufacturing environments.

Please can you introduce Arxspan?

Arxspan is a fully integrated cloud platform for scientific data management that combines chemistry and biology data in one system. It is designed to enhance collaborative research across internal teams and external partners.

The electronic laboratory notebook, or the ELN, is entirely web-based. It is easy to use and can be deployed globally within minutes. It has scientific workflow solutions embedded while enabling integration with other systems and software and built-in infrastructure and data security. This allows for data sharing internally and externally, and it also follows legal and regulatory compliance.

This is also integrated with our registration application and enables unique chemical and biological entities to be registered. The ELN also has the option to link to our inventory so you can track and manage any physical items.

Arxspan’s asset application allows users to define, collect, manage, and store asset endpoint data. This is ideal for asset development functions and low and high-throughput screening. All this data can be pulled together using our searching and reporting application.

Arxspan BioDrive, our complete solution for molecular biology, is integrated into the Arxspan ELN.

What is Arxspan BioDrive, and what makes it a versatile molecular biology solution?

The Arxspan BioDrive is a distinctive platform that empowers molecular biologists to tackle a wide range of challenges in their field. Customers can incorporate specific requirements into an experiment's configuration to fulfill their unique needs. BioDrive, with its exceptional features, offers smooth molecular biology workflows. Its efficient design and user-friendly navigation enhance the overall user experience.

Image credit: Arxspan

How can BioDrive be used to handle both DNA and RNA sequences?

BioDrive simplifies sequence handling by automatically loading sequences as double-strand DNA and generating a corresponding sequence map.

However, for more flexibility, you can choose the RNA option. When you opt for RNA, BioDrive allows you to load the sequence as single-stranded or double-stranded RNA. If you load a single-strand RNA, the sequence map will display only the forward strand.

Additionally, BioDrive features a convenient function that enables you to convert DNA into RNA. You can select either the forward or reverse strand and transform it into single-strand RNA. If you choose both strands, the RNA will be generated as double-stranded.

Moreover, BioDrive offers a unique capability for simulating splicing reactions or removing annotated introns. For instance, if your initial sequence contains introns surrounded by exons, BioDrive can remove the introns and seamlessly link the exons together, resulting in a newly formed single-strand RNA.

What features does BioDrive offer in terms of primers?

In BioDrive, managing primers is made effortless through manual addition or importing options. To manually add a primer, simply select the region of the sequence where you intend to place the primer. A dedicated primer panel allows you to assign a name, specify whether it is an RNA or DNA oligo, and choose its orientation on either the forward or reverse strand.

Furthermore, you can customize your primer by adding a dangling tail. For instance, you might append a six-nucleotide tail with a specific enzyme recognition site, such as XhoI. By copying and pasting the sequence, you can seamlessly integrate the recognition site into the primer. This modification is visually represented on the map as a dangling tail attached to the primer.

Additionally, BioDrive empowers you to make precise alterations, such as switching amino acids or codons. The binding site analysis feature enables you to assess the primer's binding potential in your DNA sequence. You can define parameters and let the system calculate the binding, helping you identify specific binding locations or potential priming sites.

Alternatively, you can import primers from a CSV file. The system allows you to customize parameters like mismatches, melting temperature (Tm), and GC content. After calculations, you are presented with multiple options that you can further refine. BioDrive gives you the flexibility to modify parameters, recalculate, and narrow down your choices. Once you have selected the desired primer, you can seamlessly integrate it into your sequence.

To ensure primer integrity, BioDrive offers a primer analysis function. By selecting 'primer analysis' under actions, you can examine the secondary structure of individual primers. If you need to assess primer dimers, you can analyze a forward primer paired with a reverse primer. The results page provides insights into the energy and the formation of homodimers.

For researchers aiming to target specific regions, BioDrive offers a comprehensive 'create primer design' feature. Here, you can define parameters such as target region, product size, and Tm range. Upon clicking 'design,' BioDrive generates a list of primer pair options, complete with detailed information, including location, TM, and GC content. This detailed overview empowers you to make informed decisions based on your research requirements.

What libraries does BioDrive offer to customers?

In BioDrive, we offer two customer libraries that function in a similar manner: the feature library and the oligo library.

The feature library enables you to create a collection of annotation features manually. You can add these features individually or use the import function to bring in a pre-existing list of annotation features. Similarly, the oligo library allows you to manage your primers or guide sequences. You have the flexibility to add them manually or import them into the library.

Once you have populated the oligo library with your sequences, you can utilize the 'detect oligos' function. This feature scans the targeting sequence and automatically adds the complementary oligo to your project. Within the 'detect oligo' action, you can customize parameters and choose from a selection of oligos to add to your scene.

Please can you tell us about BioDrive’s alignment function feature?

With the alignment function in BioDrive, you have the flexibility to either assess a sequencing file against a targeted sequence or compare two sequences directly.

You can seamlessly load multiple MBI files by dragging and dropping them onto the platform, allowing for simultaneous alignment. The aligned sequences are displayed side by side, with any non-matching nucleotide data highlighted in red. This visual cue helps identify disparities, and you can then select the specific trace and score the alignment for further analysis.

Alternatively, you can use alignment files, such as dropping a GenBank file, to compare two DNA sequences. This functionality proves invaluable when comparing sequences derived from the same origin but subjected to modifications. Again, any disparities between the sequences are highlighted in red, providing a clear visual distinction between the differences in the product sequences.

What can the re-indexing function be used for?

In BioDrive, managing circular DNA sequences and linear sequences is made effortless through the re-index function. For circular DNA, if you wish to alter the original point of the circle, you can use the re-index function to input a new location for the origin. Similarly, if you need to renumber a linear sequence, this can also be achieved using the re-index function.

Additionally, BioDrive offers the flexibility to change the name of both DNA and RNA sequences. This feature proves invaluable in scenarios such as registering a sequence into your system. BioDrive allows you to update the number to the appropriate registration ID if you receive a hit for a registration ID. This seamless integration ensures traceability for your sequences.

How can users utilize the BioDrive history feature?

The BioDrive history displays everything you did in a particular BioDrive experiment. Every time you load the sequence, generate the sequence, or do an alignment, it is all captured.

Arxpan BioDrive : A Single Solution for all your Molecular Biology Needs

What benefits do the advanced search options provide?

With advanced search, you can select whether you want to search for a linear, circular, or both sequence. Similarly, you can select whether to search for a DNA sequence, RNA sequence, or both. Another option is to select whether you want to search for nucleotide sequences, amino acid sequences, primers, or annotation features.

The system can search for specific sequences or DNA annotation features in all BioDrive experiments. For example, if you are looking for DNA sequences containing a T7 promoter, you can easily find experiments that used this specific sequence.

Please can you summarize why molecular biologists can benefit from the BioDrive?

The BioDrive is a versatile solution to visualize, simulate, and document your molecular biology procedures. Arxspan BioDrive enables the streamlining of all kinds of molecular biology tasks, from data input to analysis.

What are the Arxspan BioDrive’s upcoming features and enhancements, and how will it keep up with emerging trends in molecular biology?

Upcoming versions of Arxspan BioDrive will introduce several new features and enhancements. These updates, like our applications, will be regularly improved. The upcoming features include retrieving sequences directly from NCBI, zooming in and out of the mini-map, split-screen, and virtual gels. More details will be coming soon.

Where can readers find more information?

For additional information, visit our Arxspan website. Explore the SciY website for details about our sister companies.

On our websites, you can stay updated on news, events, and upcoming webinars related to Arxspan and other SciY applications and services. For real-time updates, follow us on social media platforms.

We recommend downloading the desktop version of BioDrive. A free trial is available, though it is limited to a seven-day period without an activation code. For an extended trial, kindly email Arxspan support.

About the Speakers

 

About Arxspan

Arxspan is a global provider of cloud-based scientific informatics tools, founded in 2011. Our mission is to deliver cutting-edge technology solutions to customers across the globe, and we have achieved this through the release of our multi-tenant cloud ELN in the same year. Our ELN offers an enterprise-level feature set designed to support small biotech start-ups as well as global pharma.

In 2013, Arxspan collaborated with multiple customers to release the integrated Registration module, which has been a game-changer in the industry. In 2017, we released the Workflow module, which enables close coordination of compound/biologic request and fulfillment between companies and their external collaborators. Our latest addition, the Data Publisher, was launched to simplify the integration of Arxspan and other enterprise, legacy, and AI data platforms.

Today, Arxspan offers a comprehensive enterprise informatics suite comprising ELN, Chemical and Biological Registration, Chemical and Biological Inventory, and Assay Data Management, with system-wide search and reporting functionality. Our customers and users span North America, Asia, India, and Europe. We continue to deploy world-class platforms, tools, services, and best-in-class support to a rapidly growing customer base.

In 2019, Bruker Biospin acquired Arxspan as a strategic platform to bring SaaS-based enterprise tools to their customers. This acquisition has provided us with the necessary resources and support to ensure our continued success in the future.

We are excited to announce the launch of our latest product, BioDrive, which is a cloud-based platform designed to streamline the management of biological data. BioDrive provides a comprehensive solution for managing and sharing data, including genomic data, proteomic data, and bioassay data. It is designed to meet the needs of biotech and pharmaceutical companies, as well as academic institutions and research organizations.

Additionally, we are pleased to announce the latest updates to our Chemical and Reg modules. These updates include new features and functionalities that improve data management, streamline workflows, and enhance collaboration. With these updates, we continue to provide our customers with the tools they need to accelerate their research and development efforts.

At Arxspan, we are committed to delivering innovative solutions that empower our customers to achieve their goals. We look forward to continuing to serve our customers and to providing them with the best possible tools and support.


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