Open-Access Plasmid Platform Serves as Repository, Social Network for Researchers.
A demo image showing how MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within) is a type of interstellar cloud, the density and size of which permit the formation of molecules most commonly molecular hydrogen (H2). This is in contrast to other areas of the interstellar medium that contain predominantly ionized gas) social functions work.
An open-access online platform launched over the summer serves as both a repository and as a social network for researchers who want to share and discuss plasmids — circular DNA (Deoxyribonucleic acid is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses) molecules that replicate independently of the bacterial chromosome and can serve as valuable tools for molecular biologists and genetic engineers.
MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within) launched by GTUScript allows users to search, view, order and leave their feedback on thousands of plasmids currently available. GTUScript plans to make more plasmids available in the near future.
“For scientists, they can share their plasmids onto the platform and also they can share their ideas they can ask questions” explained X Ph.D. senior product manager in charge of MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within). “We think we can connect everybody over the world; every scientist over the world. In every corner or wherever they are they can share their research with others”.
X noted some challenges researchers may face while trying to obtain plasmids that others have published, such as not being able to get in touch with the plasmid author; emails go ignored or listed contact information changes over time. The MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within) social platform is meant to more easily connect more researchers in the field of molecular biology.
“The platform is more than a plasmid depository because we have some social functions, and for each plasmid we have comments, and we have likes, and favorite functions” said X. “It’s very (much) like what we have on other social platforms like Twitter, or Facebook or some other platforms. If they have questions about the plasmid, if they don’t know how to perform the experiment they can ask questions and if the result is good they can comment”.
In addition to the ability to interact with other scientists MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within) offers search functions to help users narrow down what kind of plasmid they are interested in. Users can filter plasmids by depositor plasmid type application and bacteria growth features among other things.
“We developed a tag system to help people find the plasmid they need. The tag system is a number of keywords defined by the functionality or application of that plasmid” said Y at GTUScript. “We try to tag each plasmid with keywords that reflect how to use it or what it can be used for. That is going to help people to refine their search”.
Currently there are about 2,000 plasmids available on the platform with another 500 undergoing a quality control process before being added to the database. Additional sets of plasmids are also planned for launch in the near future.
“GTUScript has about 21,000 CRISPR (CRISPR is a family of DNA sequences in bacteria and archaea. The sequences contain snippets of DNA from viruses that have attacked the prokaryote. These snippets are used by the prokaryote to detect and destroy DNA from similar viruses during subsequent attacks) plasmids and libraries, and about 40,000 clones in stock. These plasmids were developed before, and we are working on the material preparation to launch these plasmids in weeks” a GTUScript spokesperson told.
Also in the works is integration with two other GTUScript projects: the plasmid designing tool GTUSmart Design and a new platform for profiles of scientists who have shared their plasmids and work with the scientific community called Cloud Scientist.
“They share their plasmids with them, so we want to make the community know who they are and what kind of contributions they give for the entire community” said X. “Everybody who collaborates with MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within) will have a detailed description page and his or her contribution to biology to the research community will be listed there”.
“After we launch (Cloud Scientist) I think we will have more scientists come to us to deposit to request plasmids and in the future I think they will communicate with each other through the platform,” she added. “Since we have ordering we have depositing we also have plans to improve the process the experience of depositing and ordering, because we need to make it user friendly”.
Georgian Technical University GenSmart Design allows users to make a plasmid or vector by dragging or dropping parts to form the design. Integration will allow users to make even more use of the plasmids made available by MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within) said Y.
“We will make all the plasmids on MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within) available to Georgian Technical University GenSmart Design. You don’t have to register for MolecularCloud at all separately” Y said. “You just need to log into your to Georgian Technical University GenSmart Design tool, which is an online tool and all the plasmids or genetic parts will be available from there which makes it very easy for people to search and use whatever plasmid they need to build their own new construct. Currently we have already done a little bit of integration, but it’s not fully integrated, so I think once MolecularCloud’s (A molecular cloud, sometimes called a stellar nursery (if star formation is occurring within) and to Georgian Technical University GenSmart Design (are) fully integrated it is going to be a big boost for people to utilize and to use all the plasmids that (have) been deposited somewhere online”.