The detailed know-how to implement research protocols frequently remains restricted to the research group that developed the method or technology. This knowledge often exists at a level that is too detailed for inclusion in the methods section of scientific articles. Consequently, methods are not easily reproduced, leading to a loss of time and effort by other researchers. The challenge is to develop a method-centered collaborative platform to connect with fellow researchers and discover state-of-the-art knowledge. Protocols.io is an open-access platform for detailing, sharing, and discussing molecular and computational protocols that can be useful before, during, and after publication of research results.

The way life scientists communicate has hardly changed since the days of Gregor Mendel. Even though mobile and Internet technology has transformed a wide array of communication channels, academic publishing has largely resisted change. As a consequence, it is impossible to stay up-to-date with the rapidly evolving methodology in the life sciences. Most corrections and optimizations of previously-published methods are never properly communicated beyond the confines of a given laboratory. Researchers are constantly rediscovering knowledge simply due to the lack of an efficient system to communicate such findings. Protocols.io is a central platform that leverages modern web and mobile technology to facilitate easy discovery and sharing of this scientific knowledge.

The advent of metagenomic methods to sequence DNA directly from an environment has revolutionized viral ecology, making it possible to “see” natural viral communities that could not be previously studied through culture. This technological leap has enabled further innovation in: extracting and sequencing limited viral DNA from communities, enriching and sequencing wild viruses through single-cell genomics, and creating new bioinformatics methods for large-scale comparative and functional metagenomics. Yet, the knowledge for specialized techniques in viral ecology remains in a subset of labs. We present a viral ecology community forum called VERVENet that strives to increase connectivity and knowledge dissemination in viral ecology research at all levels from undergraduates to accomplished viral ecologists. Our forum leverages and refines existing software from protocols.io to enhance a researcher’s ability to: discuss and share protocols, connect with fellow community members, and learn about new and innovative research in the field. In delivering these valuable tools, VERVENet is a central resource to connect, collaborate, share and innovate for the viral ecology community. Moreover, these tools are broadly useful to any community or individual lab to promote scientific inquiry, reproduction of results, and dissemination and optimization of both molecular and bioinformatics protocols.

The Internet has enabled online social interaction for scientists beyond physical meetings and conferences. Yet despite these innovations in communication, dissemination of methods is often relegated to just academic publishing. Further, these methods remain static, with subsequent advances published elsewhere and unlinked. For communities undergoing fast-paced innovation, researchers need new capabilities to share, obtain feedback, and publish methods at the forefront of scientific development. For example, a renaissance in virology is now underway given the new metagenomic methods to sequence viral DNA directly from an environment. Metagenomics makes it possible to “see” natural viral communities that could not be previously studied through culturing methods. Yet, the knowledge of specialized techniques for the production and analysis of viral metagenomes remains in a subset of labs.  This problem is common to any community using and developing emerging technologies and techniques. We developed new capabilities to create virtual communities in protocols.io, an open access platform, for disseminating protocols and knowledge at the forefront of scientific development. To demonstrate these capabilities, we present a virology community forum called VERVENet. These new features allow virology researchers to share protocols and their annotations and optimizations, connect with the broader virtual community to share knowledge, job postings, conference announcements through a common online forum, and discover the current literature through personalized recommendations to promote discussion of cutting edge research. Virtual communities in protocols.io enhance a researcher’s ability to: discuss and share protocols, connect with fellow community members, and learn about new and innovative research in the field.  The web-based software for developing virtual communities is free to use on protocols.io. Data are available through public APIs at protocols.io.

The Gibson Assembly ® HiFi 1 Step method utilizes a blend of enzymes to assemble the DNA quickly and efficiently. The use of a High-Fidelity DNA polymerase enzyme allowsfor error free cloning resulting in a seamless construct ready for multiple downstream applications. The HiFi 1 Step method allows Gibson Assembly of up to 5 fragments using a one tube, one-step, isothermal reaction. Multiple DNA fragments can be joined with greater than 90% cloning efficiency. Large constructs up to 100kb in length can be efficiently assembled in multi stage reactions.