Team:Tongji-Software/project
PROJECT
What is Alpha Ant?
Already got a brilliant idea in metabolic engineering?
Too much information to search?
Still,
You need Alpha Ant as a guide
Alpha ant is a computational tool for pathway design and reconstruction. With full consideration of metabolic burden and some useful functions, we provide an efficient and powerful pathway design guide.
Why Alpha Ant?
Background
Pathway engineering has proven indispensible in synthetic biology for its utility in design of microbes for generating value-added products, which is also the ultimate goal of our project. The core idea is to design and reconstruct pathway for proper use, including introducing heterologous metabolic reaction into a host organism, optimizing genetic processes within cells, modeling for yield prediction, flux balance analysis and so on.
However, it’s quite a challenge to reach high yield and productivity while balancing the metabolic burden in certain organism. For example, it can require sorting through thousands of possible reactions and enzymes. Also, it requires evaluation and simulation of pathway using in silico analysis. Of course, wet-lab experiments are necessary for pathway validation.
Inspiration
After investigating into metabolic pathway engineering, we realize that there is much work to do in a certain project. Commonly, we have to do a lot of research before we get started with actual experiment, such as database search, paper reading and so on. So that’s why we come up with this idea that help synthetic biologists do previous work in some ways.
In specific, We collect metabolic data from several databases including metabolic reactions, reaction main pairs, enzyme , gene , compound and so on. In this section, we provide all the related information of metabolic pathway. When it comes to ranking criteria, we choose some reliable ones and design novel ones to make our results more convincing. As for pathway search algorithm, we choose DFS (depth first search) because of its great performance in both speed and quality.
Origin of Name: Alpha Ant
Alpha Ant stands for an efficient and convenient tool for pathway engineering. Alpha means ‘origin’. In fact, Alpha Ant is the first software equipped with the most comprehensive ranking criteria.
Recently, it impressed people by the project “Alpha GO”, which also endowed “Alpha” with intelligence. Alpha Ant means its capacity to find the most efficient metabolic pathway linking two molecules is just like the ant colony’s intelligence of quickly organizing itself to find the most efficient path to a food source once it has been discovered by scouts.
So ants are great signal detector and way finder.
Data processing
We acquire metabolic reactions, gene information from KEGG. Standard Gibbs Energy are from MetaCyc and eQuilibrator. Furthermore, we obtain compound information from KEGG , ChEBI & KnowledgeBase. Enzyme data are from BRENDA and KEGG. The small molecular drug information is from DRUGBANK. Besides, we use MayaChemTools to calculate physiochemical properties of compounds.
Since we use so many databases, we came across some problem during data processing. Most challenging thing is to string all these information together because each database has its unique ID and special data format. We tried our best to integrate all these information and we hope our software can be useful to synthetic biologists.
In specific, We collect metabolic data from several databases including metabolic reactions, reaction main pairs, enzyme , gene , compound and so on. In this section, we provide all the related information of metabolic pathway. When it comes to ranking criteria, we choose some reliable ones and design novel ones to make our results more convincing. As for pathway search algorithm, we choose DFS (depth first search) because of its great performance in both speed and quality.
Origin of Name: Alpha Ant
Alpha Ant stands for an efficient and convenient tool for pathway engineering. Alpha means ‘origin’. In fact, Alpha Ant is the first software equipped with the most comprehensive ranking criteria.
Recently, it impressed people by the project “Alpha GO”, which also endowed “Alpha” with intelligence. Alpha Ant means its capacity to find the most efficient metabolic pathway linking two molecules is just like the ant colony’s intelligence of quickly organizing itself to find the most efficient path to a food source once it has been discovered by scouts.
So ants are great signal detector and way finder.
Data processing
We acquire metabolic reactions, gene information from KEGG. Standard Gibbs Energy are from MetaCyc and eQuilibrator. Furthermore, we obtain compound information from KEGG , ChEBI & KnowledgeBase. Enzyme data are from BRENDA and KEGG. The small molecular drug information is from DRUGBANK. Besides, we use MayaChemTools to calculate physiochemical properties of compounds.
Since we use so many databases, we came across some problem during data processing. Most challenging thing is to string all these information together because each database has its unique ID and special data format. We tried our best to integrate all these information and we hope our software can be useful to synthetic biologists.