HYPE-IT Software

We have developed a web application with the aim of being a powerful tool as part of our project. It has been designed as a networking and affordable space that complement the objective of our project.

HYPE-IT Software gather many sections where users could take advantage of all the tools that integrate it. Those sections are a forum, a blog, a news feed, a complete targets database, our scoring system, a gene viewer and a hierarchy of groups. Therefore, we could say we have created a complete social network.
We have used MEAN framework (mongo, express, angular, node) to carry out the web development. We have chosen this technology and a BLL logic (Business Logic Layer), because it gathers the four most web development innovative technologies, such as Angular, that has the support of Alphabet, the Google searcher owner, or mongoDB, a NoSQL database no relational scalable database benchmark . This framework set up in 2013 and has overtaken his main rivals, as php o .net.
The business logic layer facilitates implementation of the tool in different environments. You just need to change a file to modify the persistence of the software, you can persist in oracle, in mongo or whatever you want.

Another bonus that makes our software greater than others is the use of NPM (node package manager) and Bower web package manager. Both are package managers that allow us to install code packages and certificate tools by a console that make easier the activity of development. Programming an application by components as a puzzle allows us to outsource any developed function. In our case, an example could be the scoring system, that could be shared with the developer community as a certificated package.

As a future line, we would create a package that integrates scoring system code. It would allow any development team to integrate our scoring in a easy way, installing only one component, and being always updated thanks to package manager. For the moment, we have splitted application layers and processes engine in front-end routes and API routes, we have separated the front-end back-end applications as two complementary but independent parts, We have fitted out an API public rout with the intention of consulting our scoring system. Therefore, any web server can make requests to our system score and get the results by sending a data packet in a given way to a web address established API.

Other package manager advantage is the certificated components that we have used in our development software, such as ‘passport’, a component to log in in a safety way creating cookies in web browser, or ‘pdfmake’, a component to create packages. Those open access components are highly tested by developers and ease the software development.

Finally, we have developed our site with cloudno.de hosting, a service created with the intention of promote those kinds of technologies. It is free access, so that maintenance costs would be zero.
To developw the frontend side, we bought a template developed by stepofweb (http://www.stepofweb.com/). It guarantees a friendly user appearance, a complete responsive and fluid design and compatible with IE9, IE10, IE11, Chrome, Firefox, Opera and Safari.

All in all we have created a web application with the most innovative technologies, integration in an easy way all HYPE-IT tools, that encourages ideas exchange about plant synthetic biology in a community workspace.

Data Base

Often, gene related information is available on the Internet, but people don’t always know where to look or how to search efficiently, and almost every time it is so difficult to interpret because it is not clear the function of these genes. Editing them usually leads to non desired modification. Plant proteins usually are involved in many metabolic processes simultaneously, so modifications in a particular protein could lead in a non viable plant. In other cases, those modifications lead to a fruitless variety, which many times has not an agricultural benefit. So that, many times is so difficult to know which gene a plant breeder must edit despite he knows what phenotypic trait he wants to obtain.

In HYPE-IT, we have worked hard looking for genes which knockout leads to an interesting phenotypic trait. Scientific articles web pages are full of papers where gene functions are identified, but not always are identified by knocking them out. We have only selected those articles where they have done the gene silencing, either by RNAi mediated silencing or by CRISPR/Cas9 editing, and they obtained a viable fruited plants. This allow us to avoid transgenesis because we don’t need to insert exogenous genes to obtain an enhanced plant variety.
Our database gather more than 20 different genes, which knockout leads to many different improved characteristics. All these genes are well referenced, so has been demonstrated plant viability in all the cases. However, there are many proteins that are homologous between them, so we can admit that they have the same function in other plant species. After doing Blastp exams, we finally obtained more than 200 targeting genes. This is a huge Database with a high interest for plant breeders and seedbeds.

Some gene examples of our Database are:

• Ga20 oxidase, that leads to a smaller phenotype in maize or rice. All the energy that the modified plants would have used growing up, they would harness it increasing their grain properties and production.
• TFL (terminal flower), is a key regulator of delaying flowering and regulating plant growth. Its knockdown leads to more flowering varieties.
• ACS4 is a protein involved in the route of ethylene synthesis. It catalyzes the synthesis of 1­-aminocyclopropane­-1-­carboxylic acid (ACC) from S­-Adenosyl methionine. Its knockdown leads to andromonoecy varieties.

HYPE-IT Database also include important gene related information, such as the name of the gene and the protein targeted, the paper we have based on or the NCBI accession number. It allows us to organise information in a structured way, in addition to have it interconnected with other kind of databases. Mixing our Database and Software, we are able to obtain the optimal gRNA to a specific HYPE-IT Database gene using the scoring system of our Software. The objective is to reduce steps that plant breeders should do if they wanted to enhance a plant variety giving them all sequences they should order to synthesize.

We are very glad to the result of our Database. If you want to access to it, you should sign in our external webpage, located inside HYPE-IT sofware application.

http://hypeit.cloudno.de/


We also include here our database in .xls for anyone who wants to check it:


HYPE-IT Database.xlsx


As a sample of how our Database is:

Database example