A COMBINE archive is a single file containing the various documents (and in the future, references to documents), necessary for the description of a model and all associated data and procedures. This includes for instance, but not limited to, simulation experiment descriptions, all models needed to run the simulations and associated data files. The archive is encoded using the Open Modeling EXchange format (OMEX).
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics.
In computing, a plug-in (or plugin, add-in, addin, add-on, or addon) is a software component that adds a specific feature to an existing computer program. When a program supports plug-ins, it enables customization. They function in a way that is similar to browser extensions. They can be installed separately from the browser/SynBioHub and provide additional ‘custom’ functionality to the browser/SynBioHub experience despite having a completely separate code base from the browser/SynBioHub.
The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology.
A Uniform Resource Identifier (URI) is a string of characters that unambiguously identifies a particular resource. To guarantee uniformity, all URIs follow a predefined set of syntax rules, but also maintain extensibility through a separately defined hierarchical naming scheme (e.g. http://).
Web of Registries concept i.e, the idea of multiple separate repositories linked together by shared common semantics. The Web Registry Service is a software component that supports the run-time discovery and evaluation of resources such as services, datasets, and application schemes.
A COMBINE archive is a single file containing the various documents (and in the future, references to documents), necessary for the description of a model and all associated data and procedures. This includes for instance, but not limited to, simulation experiment descriptions, all models needed to run the simulations and associated data files. The archive is encoded using the Open Modeling EXchange format (OMEX).
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics.
In computing, a plug-in (or plugin, add-in, addin, add-on, or addon) is a software component that adds a specific feature to an existing computer program. When a program supports plug-ins, it enables customization. They function in a way that is similar to browser extensions. They can be installed separately from the browser/SynBioHub and provide additional ‘custom’ functionality to the browser/SynBioHub experience despite having a completely separate code base from the browser/SynBioHub.
The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology.
A Uniform Resource Identifier (URI) is a string of characters that unambiguously identifies a particular resource. To guarantee uniformity, all URIs follow a predefined set of syntax rules, but also maintain extensibility through a separately defined hierarchical naming scheme (e.g. http://).
Web of Registries concept i.e, the idea of multiple separate repositories linked together by shared common semantics. The Web Registry Service is a software component that supports the run-time discovery and evaluation of resources such as services, datasets, and application schemes.
Download: Download plugins are available on all ‘endpoint’ pages, for example pages for components, sequences, activities, etc. Download plugins return some kind of file which is downloaded by the user.
When you’ll first install SynBioHub locally and navigate to http://localhost:7777/, you shall be directed to the setup page.
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Over there you’ll see a welcome message saying, Congratulations, SynBioHub is successfully installed!
+
When you’ll first install SynBioHub locally and navigate to http://localhost:3333/, and the setup page will appear.
+
You will see a welcome message saying, “Congratulations, SynBioHub is successfully installed!”
Then, you need to fill out some details for configuring your local instance, which are as follows:
1. Branding Your SynBioHub
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Parameter
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Description
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Instance Name
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You can give a name to your local instance as per your convenience. Try to provide something descriptive to identify the kind of parts your SynBioHub instance will store. This parameter can even be changed later.
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Pick a color
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You can also choose a colour for you SynBioHub instance. This color shall be used to theme your SynBioHub instance. The default colour for SynBioHub is hue. If you want to change it just click on the color bar. A dropdown shall appear, enabling you to choose the color your own choice.
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Write a Welcome Message
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You could also provide a welcome message for the users of your instance. This may contain a brief description of what parts does your SynBioHub contain or any other brief message that you want to give to the users about your local instance. This shall be displayed on the home page of your local instance. Html tags can also be used while writing the welcome message.
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Upload a logo
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Then, is the option of uploading a logo for your instance. For uploading a logo of your choice, just click on upload file. A popup menu shall appear and then you can choose the picture from your machine. Kindly make sure that for best results, upload a SVG or high resolution PNG image.
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Allow public account creation
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Just below the upload a logo option, is situated a check box displaying the message, allow public account creation. This shall enable all the users accessing your instance, to create an account on it and hence perform function such as creating collection, submitting various types of records, etc.. To enable public account creation, just check the box, right besides this message.
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Pick a good Instance Name that describes what the server is. You can pick a logo for the top left of the header, and you can also change the color which will be used to theme most UI elements.
+Finally you can pick if you want the instance to be pu
2. Technical Details
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Parameter
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Description
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Instance URL
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This displays where this SynBioHub instance is hosted on your machine, so we can assign URLs to your submissions. By default, it has been assumed that your instance is hosted at localhost:7777/. If your instance is not hosted over there, then you can change it.
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URI Prefix
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There is a need to know need to know how to prefix URIs of objects stored in this SynBioHub. Its default is the same as the URL, and should only be changed if you are shadowing another instance. Hence, you can change it as per your convenience.
This basically is configuration file for the OpenLink Virtuoso VDBMS Server. There is a need to know where the Virtuoso INI is stored. By default it is guessed to be /etc/virtuoso-opensource-7/virtuoso.ini. If this is not true, you can change it as per your convenience.
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Virtuoso Data Directory
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Displays the location of Virtuoso DB directory. By default it is set to /virtuoso. If this is incorrect, you can change it as per your convenience.
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You can change these, but they should already be prefilled based on your url, so we don’t recommend modifying them. If you are deploying publicly you will need to setup a reverse proxy to host both the frontend and backend at the same url and port.
3. Creating Your First User Account
You need to create a user account that will have the first privileged access to your SynBioHub local instance. For that you need to enter certain details, which are as follows:
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Option Name
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Description
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Full Name
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Enter the name of the user
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Affiliation(Optional)
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You can enter the name of the university/institute that you’re currently affiliated to
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Email Address
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Enter the Email Address, through which you want to get registered. If in future you forget your login credentials, then this shall be used for sending a recovery password for your account
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Username
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You have to enter a username of your own choice. This shall be displayed on the record page of every record that you submit
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Password
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Enter a password (preferably a strong one) for keeping your user account safe
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4. Setting up External Authorization Provider
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External authentication basically, is the use of third-party authentication sources to decide whether a user should be allowed access to a system, and often what level of access an authenticated user enjoys on a system.
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For a SynBioHub local instance, you’ve got 2 options i.e, none or google. If you’ll select none as your preferred authorisation provider then, you simply have to click continue.
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To be able to use Google for authentication, you first need to register with them. This is done at their developer console. To learn more about using google as your service provider, click here. Now, if you select google as your preferred authorisation provider, then the you have to provide certain values for the following options:
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Option Name
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Description
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Client ID
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This is an identification string that is provided to every user by google. This number is unique for each user. For an example: XXXXXXXXXXXXXXXXXXXX.apps.googleusercontent.com, this is how a client ID provided by google looks.
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Client Secret
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Client secret values are created for the app by the external authentication provider when the app is registered with the provider and it is a unique identification string.
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Redirect URL
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This is the path in your application that users are redirected to after they have authenticated with Google. The path will be appended with the authorisation code for access. It must have a protocol and cannot contain URL fragments or relative paths. Also, make sure it is not a public IP address.
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Option Name
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Description
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Full Name
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Enter the name of the user
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Affiliation(Optional)
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You can enter the name of the university/institute that you’re currently affiliated to
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Email Address
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Enter the Email Address, through which you want to get registered. If in future you forget your login credentials, then this shall be used for sending a recovery password for your account
+
+
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Username
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You have to enter a username of your own choice. This shall be displayed on the record page of every record that you submit
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Password
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Enter a password (preferably a strong one) for keeping your user account safe
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If you want to obtain your client ID and client secret, you can visit Google’s documentation for further reference.
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Once, you’ve filled all the details, click continue. This will redirect you to the home page of your SynBioHub local instance.
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All Done
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Once, you’ve filled all the details, click continue. This will redirect you to the home page of your SynBioHub local instance.
+
+Next lets get started installing some Plugins!
Several parameters essential for the smooth functioning of SynBioHub, are mentioned in this sub-section. They’re as follows:
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parameter
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Description
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1. Platform: Linux x64; 4.19.76-linuxkit
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This parameter represents the platform on which SynBioHub was built.
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2. Node Version: vXX.X.X
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This represents the node.js version, on which your local instance is running
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3. Instance Name: name_of_your_choice
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This represents the name of your SynBioHub instance. This can be changed based on your convenience.
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4. Listen Port: 7777
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When Oracle HTTP Server is started, by default, it listens for requests on port 7777 (non-SSL). If port 7777 is occupied, Oracle HTTP Server listens on the next available port number between a range of 7777-7877. Thus, if port 7777 is busy, it would listen on port 7778, and so on. To get more information on this, click here.
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5. SPARQL Endpoint: http://virtuoso:8890/sparql
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A SPARQL Endpoint is a Point of Presence on an HTTP network that’s capable of receiving and processing SPARQL Protocol requests. It is identified by a URL commonly referred to as a SPARQL Endpoint URL. To know more about SPARQl endpoints, click here.
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6. Graph Store Endpoint: http://virtuoso:8890/sparql-graph-crud-auth/
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This is the endpoint for the triplestore database where the data is stored. In this case, it is the endpoint for virtuoso.
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7. Default Graph: http://localhost:7777/public
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It is the URI prefix for the public graph in the database.
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8. Graph Prefix: http://localhost:7777/
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It is the URI prefix for all graphs in the database.
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9. Thread Pool Size:
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It is the number of threads that virtuoso is allowed to use. (But it is currently empty)
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10. Upload Limit: X mb
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Shows the maximum limit of files that you can upload at once to your instance
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+
parameter
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Description
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+
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1. Platform: Linux x64; 4.19.76-linuxkit
+
This parameter represents the platform on which SynBioHub was built.
+
+
+
2. Node Version: vXX.X.X
+
This represents the node.js version, on which your local instance is running
+
+
+
3. Instance Name: name_of_your_choice
+
This represents the name of your SynBioHub instance. This can be changed based on your convenience.
+
+
+
4. Listen Port: 7777
+
When Oracle HTTP Server is started, by default, it listens for requests on port 7777 (non-SSL). If port 7777 is occupied, Oracle HTTP Server listens on the next available port number between a range of 7777-7877. Thus, if port 7777 is busy, it would listen on port 7778, and so on. To get more information on this, click here.
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+
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5. SPARQL Endpoint: http://virtuoso:8890/sparql
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A SPARQL Endpoint is a Point of Presence on an HTTP network that’s capable of receiving and processing SPARQL Protocol requests. It is identified by a URL commonly referred to as a SPARQL Endpoint URL. To know more about SPARQl endpoints, click here.
+
+
+
6. Graph Store Endpoint: http://virtuoso:8890/sparql-graph-crud-auth/
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This is the endpoint for the triplestore database where the data is stored. In this case, it is the endpoint for virtuoso.
+
+
+
7. Default Graph: http://localhost:7777/public
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It is the URI prefix for the public graph in the database.
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+
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8. Graph Prefix: http://localhost:7777/
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It is the URI prefix for all graphs in the database.
+
+
+
9. Thread Pool Size:
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It is the number of threads that virtuoso is allowed to use. (But it is currently empty)
+
+
+
10. Upload Limit: X mb
+
Shows the maximum limit of files that you can upload at once to your instance
+
+
6.2 Graphs
This section basically displays the graph URI and its corresponding triples. You can select the number of graphs you want to view on one page as well as search for any specific graphs, with the help of search box. You can also sort the graphs on the basis of number of triples.
6.3 Log
This section displays the log file for your SynBioHub local instance. You can view 4 types of logs, which are as follows:
Error log is a record of critical errors that are encountered by SynBioHub, while in operation. Some of the common entries in an error log include table corruption and configuration corruption. Error logs in many cases serve as extremely useful tools for troubleshooting and managing systems, servers and even networks.
Error log is a record of critical errors that are encountered by SynBioHub, while in operation. Some of the common entries in an error log include table corruption and configuration corruption. Error logs in many cases serve as extremely useful tools for troubleshooting and managing systems, servers and even networks.
The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology.
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics.
ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed.
The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology.
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics.
ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed.
+
+
Inorder to submit a file you must have already submitted the collection. Once you do you can click **Submit** and it will submit to the collection just created.
@@ -269,34 +272,34 @@
4.1.2 Submitting to an Existin
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Type
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Description
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SBOL
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The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. To know more about SBOL, visit this page
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Annotated zip
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ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed. To know more about zip, visit this page
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GFF3
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The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. To know more about GFF3, click here.
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FASTA
-
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics. To know more about FATSA file format, click here
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Zip
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ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed. To know more about zip, visit this page
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+
+
+
Type
+
Description
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+
+
+
+
SBOL
+
The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. To know more about SBOL, visit this page
+
+
+
Annotated zip
+
ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed. To know more about zip, visit this page
+
+
+
GFF3
+
The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. To know more about GFF3, click here.
+
+
+
FASTA
+
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics. To know more about FATSA file format, click here
+
+
+
Zip
+
ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed. To know more about zip, visit this page
You can enter the name of the university/institute that you’re currently affiliated to
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Email Address
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Enter the Email Address, through which you want to get registered. If in future you forget your login credentials, then this shall be used for sending a recovery password for your account
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Username
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You have to enter a username of your own choice. This shall be displayed on the record page of every record that you submit
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Password
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Enter a password (preferably a strong one) for keeping your user account safe
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+
+
+
Option Name
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Description
+
+
+
+
+
Full Name
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Enter the name of the user
+
+
+
Affiliation(Optional)
+
You can enter the name of the university/institute that you’re currently affiliated to
+
+
+
Email Address
+
Enter the Email Address, through which you want to get registered. If in future you forget your login credentials, then this shall be used for sending a recovery password for your account
+
+
+
Username
+
You have to enter a username of your own choice. This shall be displayed on the record page of every record that you submit
+
+
+
Password
+
Enter a password (preferably a strong one) for keeping your user account safe
On the search results page, there is button labeled as sequence search. Clicking on that button will direct you to a page containing a list of sequence search options. To search using a sequence, you can provide the values for the options, as described in the table below:
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Option Name
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Description
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Enter Sequence
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Enter the sequence or upload a FASTA/FASTQ file, by clicking the choose file option just below the box. This shall search only for exact matches of the sequence. Your entry must be the first key/value pair
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Search Method
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You can choose the perspective of your search. You can perform a global search or an exact search. The exact search shall display, those records which are an exact match to the sequences that you’ve entered and the global search search will display those results which have even the smallest of the similarities to the sequence that you’ve entered.
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Number of Results
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You may customise the number of results, the value for which must not exceed 10,000. This translates into the maximum number of hits to accept before stopping the search. Kindly note that, higher the value, the longer the runtime.
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Minimum Sequence Length
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You need to enter the minimum sequence length. This value basically specifies the minimum length of the sequence, which you want to search for. Values for this parameter should not exceed 100,000.
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Maximum Sequence Length
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You need to enter the maximum sequence length. This value basically specifies the maximum length of the sequence, which you want to search for. Values for this parameter should not exceed 100,000.
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# of failed hits before stopping
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Then, you need to enter the maximum number of non-matching target sequences, that are to be considered before the search is halted. This option works in pair with the flag above. The search process sorts the target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if none of the first x examined target sequences pass the acceptation criteria, the search process stops for that query (no hit). If this flag is set to a higher value, more target sequences are considered. If the flag above and this flag are both set to 0, the complete database is searched.
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Percent Match
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Then, we have is the percentage match, which has a value between 0 and 1. This is the value of pairwise identity that must match with the sequence, otherwise the sequence is rejected.
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Pairwise Identity Definition
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You may select the value for this attribute from the following options: 1) Default: Edits distance excluding the terminal gaps, 2) CD-HIT definition: Considers the following ratio: (matching columns) / (shortest sequence length), 3) Marine Biological Lab definition: counts each gap opening (internal or terminal) as a single mismatch, whether or not the gap was extended: 1.0 - [(mismatches + gap openings)/(longest sequence length)], 4) BLAST Definition: equivalent to edit distance for global pairwise alignments
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+
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Option Name
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Description
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+
+
+
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Enter Sequence
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Enter the sequence or upload a FASTA/FASTQ file, by clicking the choose file option just below the box. This shall search only for exact matches of the sequence. Your entry must be the first key/value pair
+
+
+
Search Method
+
You can choose the perspective of your search. You can perform a global search or an exact search. The exact search shall display, those records which are an exact match to the sequences that you’ve entered and the global search search will display those results which have even the smallest of the similarities to the sequence that you’ve entered.
+
+
+
Number of Results
+
You may customise the number of results, the value for which must not exceed 10,000. This translates into the maximum number of hits to accept before stopping the search. Kindly note that, higher the value, the longer the runtime.
+
+
+
Minimum Sequence Length
+
You need to enter the minimum sequence length. This value basically specifies the minimum length of the sequence, which you want to search for. Values for this parameter should not exceed 100,000.
+
+
+
Maximum Sequence Length
+
You need to enter the maximum sequence length. This value basically specifies the maximum length of the sequence, which you want to search for. Values for this parameter should not exceed 100,000.
+
+
+
# of failed hits before stopping
+
Then, you need to enter the maximum number of non-matching target sequences, that are to be considered before the search is halted. This option works in pair with the flag above. The search process sorts the target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if none of the first x examined target sequences pass the acceptation criteria, the search process stops for that query (no hit). If this flag is set to a higher value, more target sequences are considered. If the flag above and this flag are both set to 0, the complete database is searched.
+
+
+
Percent Match
+
Then, we have is the percentage match, which has a value between 0 and 1. This is the value of pairwise identity that must match with the sequence, otherwise the sequence is rejected.
+
+
+
Pairwise Identity Definition
+
You may select the value for this attribute from the following options: 1) Default: Edits distance excluding the terminal gaps, 2) CD-HIT definition: Considers the following ratio: (matching columns) / (shortest sequence length), 3) Marine Biological Lab definition: counts each gap opening (internal or terminal) as a single mismatch, whether or not the gap was extended: 1.0 - [(mismatches + gap openings)/(longest sequence length)], 4) BLAST Definition: equivalent to edit distance for global pairwise alignments
+
+
After filling up the desired options, press the search button to get the search results.
1.3 Advanced Search
On the search results page, there is collumn on the left hand side it contains a list of advanced search options. To search using advanced parameters, you can provide the values for the option as described in the table below. The records that’ll be displayed will match all of the criteria, that you’ll fill in. Kindly note that you don’t need to fill in all of the options. The options are as follows:
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Option Name
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Description
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Object Type
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The type of the record you want to search for i.e, a collection, design, activity, etc…
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Creator
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The username of the record’s creator
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Created After and Created Before
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The timeframe in which the record was created. Make sure to enter the dates in the YYYY-MM-DD format
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Modified After Modified Before
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The timeframe in which the record was last modified. Make sure to enter the dates in the YYYY-MM-DD format
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ID/Name/Description
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Enter the ID or the name or the description of the record, which you want to search for
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Type
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Select the type of the record, from the following available options in the dropdown menu, for an example: No filter, biopax:Complex, biopax:DnaRegion, biopax:Protein, so:circular, etc…
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Role
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select the role of the record from this dropdown menu. It contains various sub-categories of igem or SO.
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Collections
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You may select any number of collections, based on your convenience. To select a collection, click on the value attribute of collection and select it from the drop down menu
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Customisable Filters
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You may apply customised filters for the design you want to search for. For that purpose, click add filter and a drop down menu will appear having various parameters for filtering. These parameters are basically, the properties for filtering the records. Select the property that you want your record to be filtered by, and then click on filter. This shall reload the page and then select the value of the filter, from the drop down on the right hand side. You may provide as many as 5 customised filters which’er optional
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Option Name
+
Description
+
+
+
+
+
Object Type
+
The type of the record you want to search for i.e, a collection, design, activity, etc…
+
+
+
Creator
+
The username of the record’s creator
+
+
+
Created After and Created Before
+
The timeframe in which the record was created. Make sure to enter the dates in the YYYY-MM-DD format
+
+
+
Modified After Modified Before
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The timeframe in which the record was last modified. Make sure to enter the dates in the YYYY-MM-DD format
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ID/Name/Description
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Enter the ID or the name or the description of the record, which you want to search for
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Type
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Select the type of the record, from the following available options in the dropdown menu, for an example: No filter, biopax:Complex, biopax:DnaRegion, biopax:Protein, so:circular, etc…
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Role
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select the role of the record from this dropdown menu. It contains various sub-categories of igem or SO.
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Collections
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You may select any number of collections, based on your convenience. To select a collection, click on the value attribute of collection and select it from the drop down menu
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Customisable Filters
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You may apply customised filters for the design you want to search for. For that purpose, click add filter and a drop down menu will appear having various parameters for filtering. These parameters are basically, the properties for filtering the records. Select the property that you want your record to be filtered by, and then click on filter. This shall reload the page and then select the value of the filter, from the drop down on the right hand side. You may provide as many as 5 customised filters which’er optional
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After selecting the desired options for performing a search using advanced parameters, click search. This will return the records after comprehending all the details that you’ve entered.
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1.3 Advanced Search
Just below, there is an option to create a new collection as well. If you wish to create a collection from your search results, you need to fill in the following items:
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Option Name
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Description
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Collection Name
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This is the name string that’ll be assigned to the submission.
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Collection Description
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This is the description string that briefly explains your submission.
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Collection ID
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This is a user-defined alphanumeric string identifier for the submission and it should contain alphanumeric and underscores characters only.
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Collection Version
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This is the alphanumeric string which is associated with the submission.
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Option Name
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Description
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Collection Name
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This is the name string that’ll be assigned to the submission.
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Collection Description
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This is the description string that briefly explains your submission.
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Collection ID
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This is a user-defined alphanumeric string identifier for the submission and it should contain alphanumeric and underscores characters only.
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Collection Version
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This is the alphanumeric string which is associated with the submission.
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After you’ve filled in all the available options, click on create collection. This will return the search results to you, in the form a private collection.
This contains the name of each and every record that is in that collection, that is provided by the user who had submitted that particular record. Just besides the header there is small figure, clicking on which shall sort this table on the basis of reverse priority of alphabets i.e, Z-A
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Identifier
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This contains the ID or the identifier of that particular record,that is provided by the user who had submitted that particular record. ust besides the header there is small figure, clicking on which shall sort this table on the basis of reverse priority of alphabets i.e, Z-A
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Type
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This represents the type of the record, i.e. whether it is a module, sequence, activity, etc.
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Description
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This is a brief description, that is provided by the user, who’d submitted that particular records. This description, in brief describes, what that particular record does.
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Table Header
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Description
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Name
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This contains the name of each and every record that is in that collection, that is provided by the user who had submitted that particular record. Just besides the header there is small figure, clicking on which shall sort this table on the basis of reverse priority of alphabets i.e, Z-A
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Identifier
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This contains the ID or the identifier of that particular record,that is provided by the user who had submitted that particular record. ust besides the header there is small figure, clicking on which shall sort this table on the basis of reverse priority of alphabets i.e, Z-A
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Type
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This represents the type of the record, i.e. whether it is a module, sequence, activity, etc.
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Description
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This is a brief description, that is provided by the user, who’d submitted that particular records. This description, in brief describes, what that particular record does.
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2.1.3 Viewing a Module (Definition)
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2.1.3 Viewing a Module (Definition)
Just below the clickable options, the VisBol navigator is located, which displays the structure of that particular module. VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL Navigator also has zooming capabilities. This, graphically represents the structure of the module. By hovering your pointer over this structure, you can view the following attributes of that particular module i.e, type of resource, identifier, name and role of the module.
Then, what we have is the section titled, functional components. A FunctionalComponent is an instance of a ComponentDefinition being used as part of a ModuleDefinition. The ModuleDefinition describes how the that describes how the FunctionalComponent interacts with others and summarizes their aggregate function. The parameters included in this section are described in the table below:
1) Access: The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo on another ComponentInstance or Module contained by a different parent ComponentDefinition or ModuleDefinition (one that does not contain this ComponentInstance). 2) Direction:Each FunctionalComponent MUST specify via the direction property whether it serves as an input, output, both, or neither for its parent ModuleDefinition object.
1) Definition: The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. ComponentDefinition effectively provides information about the types and roles of the ComponentInstance. 2) MapsTo: When ComponentDefinition and ModuleDefinition objects are composed into structural and functional hierarchies using ComponentInstance and Module objects, it is often the case that some ComponentInstance objects are intended to represent the same entity in the overall design. The purpose of the MapsTo class is to make these identity relationships clear and explicit. For example, consider a ModuleDefinition for a genetic inverter that includes a FunctionalComponent for an abstract repressor protein. When this ModuleDefinition is instantiated within a “higher level” ModuleDefinition that includes a FunctionalComponent for a LacI protein, the MapsTo object can be used to indicate that the repressor protein in the first ModuleDefinition is LacI in the context of the composite design.
1) Public: Indicates that a ComponentInstance MAY be referred to by remote MapsTo objects. 2) Inout: Indicates that the FunctionalComponent is both an input and output.
1) Access: The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo on another ComponentInstance or Module contained by a different parent ComponentDefinition or ModuleDefinition (one that does not contain this ComponentInstance). 2) Direction:Each FunctionalComponent MUST specify via the direction property whether it serves as an input, output, both, or neither for its parent ModuleDefinition object.
1) Definition: The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. ComponentDefinition effectively provides information about the types and roles of the ComponentInstance. 2) MapsTo: When ComponentDefinition and ModuleDefinition objects are composed into structural and functional hierarchies using ComponentInstance and Module objects, it is often the case that some ComponentInstance objects are intended to represent the same entity in the overall design. The purpose of the MapsTo class is to make these identity relationships clear and explicit. For example, consider a ModuleDefinition for a genetic inverter that includes a FunctionalComponent for an abstract repressor protein. When this ModuleDefinition is instantiated within a “higher level” ModuleDefinition that includes a FunctionalComponent for a LacI protein, the MapsTo object can be used to indicate that the repressor protein in the first ModuleDefinition is LacI in the context of the composite design.
1) Public: Indicates that a ComponentInstance MAY be referred to by remote MapsTo objects. 2) Inout: Indicates that the FunctionalComponent is both an input and output.
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Subsequently, just below the functional components we have the Interactions section. Interaction basically, provides a more detailed description of how the FunctionalComponent objects of a ModuleDefinition are intended to work together. It has a table consisting of the following attributes:
1) Interaction: Provides more detailed description of how the FunctionalComponent objects of a ModuleDefinition are intended to work together. 2) Participation: Each Participation represents how a particular FunctionalComponent behaves in its parent Interaction.
The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance.
1) Type: Specifies the category of biochemical or physical entity. For example DNA, protein, or small molecule that a ComponentDefinition object abstracts for the purpose of engineering design. For DNA or RNA entities, additional types fields are used to describe nucleic acid topology (circular / linear) and strandedness (double- or single-stranded). 2) Role: Clarifies the potential function of an entity in a biochemical or physical context. When it is used for ComponentDefinitions, it MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO). It may be a product, genetic production, template, etc.
1) Interaction: Provides more detailed description of how the FunctionalComponent objects of a ModuleDefinition are intended to work together. 2) Participation: Each Participation represents how a particular FunctionalComponent behaves in its parent Interaction.
The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance.
1) Type: Specifies the category of biochemical or physical entity. For example DNA, protein, or small molecule that a ComponentDefinition object abstracts for the purpose of engineering design. For DNA or RNA entities, additional types fields are used to describe nucleic acid topology (circular / linear) and strandedness (double- or single-stranded). 2) Role: Clarifies the potential function of an entity in a biochemical or physical context. When it is used for ComponentDefinitions, it MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO). It may be a product, genetic production, template, etc.
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2.1.4 Viewing a Component (Definition)
Component (Definition) is used to represent biological design components such as DNA, RNA and small molecules. Once you’ve successfully navigated to the component’s home page, other than the parameters described in the general section, you’ll be able to view a few other parameters, which are described below.
Just below the details table, you’ll be able to view a table titled, components, which has the following parameters:
The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo on another ComponentInstance or Module contained by a different parent ComponentDefinition or ModuleDefinition (one that does not contain this ComponentInstance)
The ComponentInstance abstract class is inherited by SBOL classes that represent the usage or occurrence of a ComponentDefinition within a larger design (that is, another ComponentDefinition or ModuleDefinition).
The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance.
The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo on another ComponentInstance or Module contained by a different parent ComponentDefinition or ModuleDefinition (one that does not contain this ComponentInstance)
The ComponentInstance abstract class is inherited by SBOL classes that represent the usage or occurrence of a ComponentDefinition within a larger design (that is, another ComponentDefinition or ModuleDefinition).
The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance.
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Below the components table is another table titled, sequence annotations, having the following attributes:
The SequenceAnnotation class describes one or more regions of interest on the Sequence objects referred to by its parent ComponentDefinition. In addition, SequenceAnnotation objects can describe the substructure of their parent ComponentDefinition through association with the Component objects contained by this ComponentDefinition.
1) Components: The components property is OPTIONAL and MAY specify a set of Component objects that are contained by the ComponentDefinition. The set of relations between Component and ComponentDefinition objects is strictly acyclic. 2) Role: Clarifies the potential function of an entity in a biochemical or physical context. When it is used for ComponentDefinitions, it MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO).
The SequenceAnnotation class describes one or more regions of interest on the Sequence objects referred to by its parent ComponentDefinition. In addition, SequenceAnnotation objects can describe the substructure of their parent ComponentDefinition through association with the Component objects contained by this ComponentDefinition.
1) Components: The components property is OPTIONAL and MAY specify a set of Component objects that are contained by the ComponentDefinition. The set of relations between Component and ComponentDefinition objects is strictly acyclic. 2) Role: Clarifies the potential function of an entity in a biochemical or physical context. When it is used for ComponentDefinitions, it MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO).
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2.1.5 Viewing a Sequence
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2.2 Downloading the Information
Following are the types of formats that you may be able to download a record:
Note: Not all the record types may be downloaded in all formats.
The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology.
A COMBINE archive is a single file containing the various documents (and in the future, references to documents), necessary for the description of a model and all associated data and procedures. This includes for instance, but not limited to, simulation experiment descriptions, all models needed to run the simulations and associated data files. The archive is encoded using the Open Modeling EXchange format (OMEX).
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics.
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Image
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Image is a capture of the Visbol display at the top of the page.
The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology.
A COMBINE archive is a single file containing the various documents (and in the future, references to documents), necessary for the description of a model and all associated data and procedures. This includes for instance, but not limited to, simulation experiment descriptions, all models needed to run the simulations and associated data files. The archive is encoded using the Open Modeling EXchange format (OMEX).
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics.
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Image
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Image is a capture of the Visbol display at the top of the page.
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Additional download options may be available via the use of download plugins.
