Uncategorized — 01 July 2015

By Yael Lederman

Everyday, biologists seek simple answers to life’s most complex questions. But getting from point A to point B can be a painstaking process. Software, a way to organize the chaos into simple, easy-to-use interface, is the impetus for scientific growth. With many different types of software on the market, understanding which software works for you is a science in itself. Let me simplify the process for you by comparing the DNA editing giant Vector NTI with the emerging software platform Genome Compiler.

Compatibility

The first step when deciding which software to use is knowing whether it can be downloaded onto your computer. Genome Compiler has both an online version and a downloadable version both available for Windows and Mac. Identical in function, these two options allow users to design DNA everywhere without limitations. Vector NTI has two versions on the market: Advanced and Express, which are both solely downloadable and not available online. Differing vastly, both versions also have different compatibilities. For example, the Advanced version can be downloaded onto a Mac computer whereas the Express version is available solely for Windows users.

Price

As scientists constantly working with strict budgets, the next step will most likely be assessing whether the price is right. Genome Compiler’s software is and will always be free to academics, a business model that Genome Compiler prides itself on. How do they make their money? Simple. Users work on the platform for free. When they purchase services through the system, Genome Compiler gets a cut from the providers. Not to worry though, the user’s price remains the same! Enterprise customers get different deals. Vector NTI has been a giant in the market even before smaller companies like Genome Compiler began emerging in the 2010s. For that reason, they have the luxury of charging upwards of $1,000/year depending on usage. Discounts are available for Academia, but there’s no better discount than free!

Tools

When you’ve assessed compatibility and price, the next hurdle to cross is the power in the product – what are the available features and are they the one’s you need? Vector NTI was a software company acquired by the sizeable Life Technologies over a decade ago. Vector NTI monopolized the market at the time, developing features and building additional ones over time, eventually leading to its acquisition by Thermo Fisher Scientific Inc. As one of the oldest companies in the industry, Vector NTI has had the most time to develop the most features. For this reason, they win the quantity battle. Genome Compiler, the agile newbie in the market, wins the quality battle. Although outcompeted in number by the vast library of Vector NTI features, Genome Compiler has been refining the few most-used, most-relevant features, and optimizing them for the constantly changing industry.
Here’s a few examples:

  • Vector NTI has many fairly convoluted wizards that attempt to guide scientists through DNA design methods. Genome Compiler has the two most common (Gibson Assembly and Restriction Ligation), which are both user friendly and truly simplifying.
  • Gel simulation, a Vector NTI feature that provides users with a lab-like representation of the data they already have, does not provide vital additional information to the user and is therefore absent in the Genome Compiler software.
  • Vector NTI has a strong protein and RNA platform, whereas Genome Compiler focuses mostly on cloning.

Customer Support

Software can have all the most important features, but if you don’t know how to use them, they become futile. As a company, Genome Compiler focuses on retaining users by enhancing consumer satisfaction. The excellent and free user tutorials provide a seamless transition so the user can begin working quickly without tremendous effort. Genome Compiler also offers online chat support, an automated user guide, and hints that guide you as you work. Being a small and agile new company, Genome Compiler also provides an open forum with its users, where you can ask for new features or give feedback on existing features. Genome Compiler uses this information to refine their product, bridging the gap between customer and company. New Vector NTI users have access to user guides, although tutorials are harder to find. Additionally, the backing of a large, established company like Thermo Fisher is definitely advantageous in terms of reliability. But using software developed by a company that focuses mostly on other sectors can be difficult, especially as a new user. Simply put, Vector NTI can tell you how to navigate while Genome Compiler can hold your hand and walk with you.

User Friendliness

Looks aren’t everything, but I think we can all agree that they hold some bearing. Interface should be appealing and functional. While Vector NTI has countless great features that allow scientists to do powerful work, the software itself is difficult to dive into as a new user. Although initially it is aesthetically convoluted, with what feels like too many unmarked buttons, veteran users seem to like the interface when they’ve learned it; many proud users even mark VectorNTI as a skill on LinkedIn. Vector NTI has recently come out with newer versions of its express software with nicer user interface, hinting at the possibility of improvement. Still, Genome Compiler’s look is newer and fresher, making it simple to navigate through the software as a new user.

Special Features

Both companies work to help make their product functional for users, but each has a different focus. Genome Compiler is a small, forward-looking start-up while Vector NTI is the large, firmly settled software. Genome Compiler’s “newness” provides an advantage in its outlook towards the future. It has worked to provide advanced features that may be vital in the future of biotechnology. For example, in order to minimize errors and optimize productivity, Genome Compiler developed a validation feature called “compilation” that allows users to find errors in their sequences based on specific, previously set parameters. The software will warn the user about violations. For example, if there is a frame shift in their sequence. Another feature, combinatorial design, allows users to list alternatives for different parts of the sequence without altering it. The software also tracks changes much like a Google document. These simple and powerful features could have a profound effect on the uses of the software in the future. Vector NTI is reliable for its long-standing place in the market and the backing of the Thermo Fisher, but it isn’t as forward thinking as the fresh start up which could become a challenge for them as the biotech industry matures. They do have several features, though, that work to simplify user experience like the 3D Molecule Viewer for visualizing protein structure and their reverse complement tool that gives users a list of affected features. In the end, the essential difference is in each company’s focus. Where Genome Compiler is personal, Vector NTI is global; both companies focus on different consumer needs. Vector NTI develops tools that are dominant in the biotech industry while Genome Compiler develops its features based on direct user feedback.

Database/Library

The options for sequences, vectors, and plasmids should also play a role in determining the best software for you. Here, Vector NTI comes out on top, with many more options for genomes, vectors, synthetic sequences, etc. With more options comes more power to design diverse DNA. Genome Compiler, on the other hand, is constantly growing, partnering with new companies to enhance their user’s options – iGEM, NCBI, AddGene, Sigma-Aldrich to name a few. Because it is a fairly new company, it is clear that they are far from plateauing and constantly growing. They also allow users to easily import additional data. Although they have fewer options, Genome Compiler presents their options in a more user-friendly way. For example, their library is constantly on-screen, available to drag and drop whenever needed. Vector NTI hides their extensive database, always a few clicks away, making it tedious to go back and forth between screens.

CONCLUSIONS

The industry giant Vector NTI might be overrun if it doesn’t watch it’s back. Although still very powerful and teaming with versatile features and databases, their interface is becoming outdated in a modern world where simplicity reigns. Agile competitors like Genome Compiler offer users a personal, user-friendly product that’s more adaptable to new emerging needs in the market. Presently, Vector NTI is powerful, allowing scientists to design more with access to larger, expansive libraries. The smaller software-focused company Genome Compiler that pays more attention to user wants and needs is quickly gaining traction. The Genome Compiler allows users to learn the software quicker, design more readily and simply, while designing powerful DNA with the market’s most relevant features for free. For the user, choosing comes down to your needs. Whether you need diverse features and the complexity of Vector NTI doesn’t faze you or whether you’re more enticed by the simple and intuitive, yet powerful interface of Genome Compiler, there’s software out there for you. So stop reading and get working.

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Yael Lederman

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