Difference between revisions of "Team:SJTU-software/Description"

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         <!-- MAIN-->
 
         <!-- MAIN-->
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          <div id="main" class="cf">
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<div class="headline">
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                    Project —— Description     
 +
                </div>
 +
                    <!-- posts list -->
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                    <div id="posts-list" class="cf">
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 +
                        <article class="cf" id="Background">
 +
                           
 +
                            <div class="entry-title">
 +
                                <div class="post-heading" >BACKGROUND</div>
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                With the development of experimental techniques such as yeast two-hybrid, mass spectrometry, chromosome immunoprecipitation, tandem affinity purifica-tion, protein chip, phage display and literature mining, a large number of mo-lecular interaction data, also known as biological network data, such as protein interaction network, metabolic network, Gene expression network, gene regula-tory network and signal transduction network have been generated. And these data showed an exponential growth trend. 
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                Nowadays, a great deal of research work on biological network data has been carried out.Among them, one of important researches is the comparative analy-sis of biological network data,  the alignment of biological networks.Through the alignment, we can understand and study organisms, find the correlation between their structure and function, study the evolution and evolution of organisms based on the comparison results of biological network data, and transfer knowledge between different networks. With unknown organisms, we study un-known organisms.
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                At present, most of the research work is only for a specific problem or applica-tion, the time complexity of the algorithm is high, and  the algorithm is Ineffi-cient.The aim of the research on alignment models and algorithms of biological networks is to develop a general-purpose alignment software, which can effi-ciently align multiple biological networks with multiple application patterns, similar to the sequence alignment software BLAST.
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                At the same time, the Systems Biology Markup Language(SBML), a representa-tion and standard format representing many different classes of biological phe-nomena, including metabolic networks, cell signaling pathways, is frequent-ly used and visualized. There are currently three Levels of SBML defined. SBML is defined in Levels. However, each Level can have multiple Versions within it, and new Versions of a Level dosupersede old Versions of that same Level. Therefore, it is neces-sary to be compared in different versions.
 +
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 +
                            <!-- <div class="feature-image">
 +
                              <img src="images/HP/BUDS2.jpg" alt="Thumbnail" />
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                            </div> -->
 +
                   
 +
                        </article>
 +
                       
 +
                        <article class="cf" id="What">
 +
                            <div class="entry-title">
 +
                                    <div class="post-heading" >WHAT IS METLAB ?</div>
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                METLAB is an online integrated Toolbox, focusing on more efficient network alignment and more convenient model visualization. Due to requirement we found in actual study ,several bioinformatics tools are integrated into METLAB , to  help users research more effectively. The interface is terse, friendly and can be used  conveniently with steady and safe in motion. Simply choose one func-tion,  upload the .met file and run, users can get what they need.
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                One of the primary functions in Metlab is biological network alignment, present-ed in a friendly way.. It makes it accessible to make comparisons between local pathway and online pathways, in order to get the whole picture. Its metabolic networks model  is constructed on the basis of BiGG. With  just  one  click,  users  can  obtain  a  analysis  report  for  their  pathway, which is defined by metabolite reaction.  Metlab can also be used to visualize SBML model and com-pare different versions of SBML model. And another function is SMILES’s visualization.
 +
                            </div>
 +
                            <!-- <div class="excerpt">
 +
                                pharetra.
 +
                            </div> -->
 +
                         
 +
                        </article>
  
 +
                        <article class="cf" id="How">
 +
                            <div class="entry-title">
 +
                                    <div class="post-heading" >HOW TO USE IT?</div>
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                Visit <a href="http://metlab-sjtu.com" target="_blank" >http://metlab-sjtu.com </a>.
 +
                            </div>
 +
                            <div class="feature-image">
 +
                                <img src="images/project/METLAB.jpg" alt="Thumbnail" />
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                Select the function in need on the page.
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                Upload the .met file.
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                Have a try!
 +
                            </div>
 +
                         
 +
                        </article>
 +
                       
 +
                    </div>
 +
                    <!-- ENDS post list -->
 +
                   
 +
                    <!-- SIDEBAR -->
 +
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 +
                   
 +
                        <ul>
 +
                            <li class="block">
 +
                                <h4 class="heading">Description</h4>
 +
                                <ul>
 +
                                    <li class="cat-item"><a href="#Background" >BACKGROUND</a></li>
 +
                                    <li class="cat-item"><a href="#What" >WHAT IS METLAB?</a></li>
 +
                                    <li class="cat-item"><a href="#How" >HOW TO USE IT?</a></li>
 +
                                </ul>
 +
                            </li>
 +
                        </ul>
 +
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 +
                    <!-- ENDS SIDEBAR -->
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         <!-- ENDS MAIN -->
 
         <!-- ENDS MAIN -->
 
 

Revision as of 12:05, 12 October 2018

SJTU-software
Metlab: a metabolic network research tool box
Project —— Description
BACKGROUND
With the development of experimental techniques such as yeast two-hybrid, mass spectrometry, chromosome immunoprecipitation, tandem affinity purifica-tion, protein chip, phage display and literature mining, a large number of mo-lecular interaction data, also known as biological network data, such as protein interaction network, metabolic network, Gene expression network, gene regula-tory network and signal transduction network have been generated. And these data showed an exponential growth trend.
Nowadays, a great deal of research work on biological network data has been carried out.Among them, one of important researches is the comparative analy-sis of biological network data, the alignment of biological networks.Through the alignment, we can understand and study organisms, find the correlation between their structure and function, study the evolution and evolution of organisms based on the comparison results of biological network data, and transfer knowledge between different networks. With unknown organisms, we study un-known organisms.
At present, most of the research work is only for a specific problem or applica-tion, the time complexity of the algorithm is high, and the algorithm is Ineffi-cient.The aim of the research on alignment models and algorithms of biological networks is to develop a general-purpose alignment software, which can effi-ciently align multiple biological networks with multiple application patterns, similar to the sequence alignment software BLAST.
At the same time, the Systems Biology Markup Language(SBML), a representa-tion and standard format representing many different classes of biological phe-nomena, including metabolic networks, cell signaling pathways, is frequent-ly used and visualized. There are currently three Levels of SBML defined. SBML is defined in Levels. However, each Level can have multiple Versions within it, and new Versions of a Level dosupersede old Versions of that same Level. Therefore, it is neces-sary to be compared in different versions.
WHAT IS METLAB ?
METLAB is an online integrated Toolbox, focusing on more efficient network alignment and more convenient model visualization. Due to requirement we found in actual study ,several bioinformatics tools are integrated into METLAB , to help users research more effectively. The interface is terse, friendly and can be used conveniently with steady and safe in motion. Simply choose one func-tion, upload the .met file and run, users can get what they need.
One of the primary functions in Metlab is biological network alignment, present-ed in a friendly way.. It makes it accessible to make comparisons between local pathway and online pathways, in order to get the whole picture. Its metabolic networks model is constructed on the basis of BiGG. With just one click, users can obtain a analysis report for their pathway, which is defined by metabolite reaction. Metlab can also be used to visualize SBML model and com-pare different versions of SBML model. And another function is SMILES’s visualization.
HOW TO USE IT?
Visit http://metlab-sjtu.com .
Thumbnail
Select the function in need on the page.
Upload the .met file.
Have a try!

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