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2008-08-10 06:23:05 UTC
<p style="text-align:justify"><span style="font-size: medium; "><span style="font-family: Arial; ">This group is intended to foster sharing of biomashups: bioinformatics flavoured mashups authored for one of the major mashup frameworks, Popfly (www.popfly.com). Components, pipes, blocks, JS pages and blocks of any kind are welcome, but we have a particular interest in blocks created under Popfly as it supports a convenient visual composition of component blocks.</span></span></p>
<p style="text-align:justify"><span style="font-size: large; "><span style="font-weight: bold; ">What are mashups?</span></span></p>
<p style="text-align:justify"><span style="font-size: medium; "><span class="Apple-style-span">Bioinformatics analysis involves the use of many software tools and databases that are accessed through a variety of websites. Integration of these disparate resources is required for efficient analysis as one bioinformatics problem may require the use of a number of these different tools and databases. Mashups offer a new avenue for performing bioinformatics analysis. A mashup is a web application that combines data and services from multiple sources, and can therefore allow for the integration of various bioinformatics tools to perform a specific task efficiently.</span></span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: medium; "><span class="Apple-style-span">A number of mashup frameworks are available: Google Mashups, Yahoo Pipes and Microsoft Popfly. The Popfly framework is based around a basic service unit termed a block. These blocks can be combined to form a mashup through a simple drag-and-drop mechanism, with connections being formed between the relevant blocks as required. Popfly is particularly convenient as a vehicle for re-use as once they are created, blocks can be shared with the bioinformatics community for reuse in other mashups as necessary.</span></span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: large; "><span class="Apple-style-span" style="font-weight: bold; ">Popfly Blocks</span></span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: medium; "><span class="Apple-style-span">A Popfly block makes use of a Javascript file, which provides methods for user generated code to invoke. It also has an associated XML manifest file which describes more about the block. Popfly blocks each perform a specific task within a mashup, receiving input either from the user, or from other blocks in a mashup and generating output which is either displayed, or passed to another block for further processing. Popfly blocks that we have developed for biomashups are available here, in the shared files for the BioMashups group, and are also available to registered users at Popfly. Block functions include user input blocks, blocks for displaying mashup results and bioinformatics processing blocks, which access bioinformatics data sources. Processing blocks can perform tasks such as retrieval of relevant information from a bioinformatics database (egs GenBank or UniProt) and accessing prediction tools, such as those which predict functional or structural characteristics of a protein. Example blocks include:</span></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li style="text-align:justify;"><span style="font-size:11.0pt;font-family:Arial">User Input Protein: receives input from the user in the form of either a Uniprot protein ID or a protein sequence</span></li>
<li style="text-align:justify;"><span style="font-size:11.0pt;font-family:Arial">Protein Characteristics: takes a protein ID as input and returns information about the protein from the Uniprot database. <span style="mso-spacerun:yes"> </span></span></li>
<li style="text-align:justify;"><span style="font-size:11.0pt;font-family:Arial">Blast: makes a protein sequence comparison using Blast and provides a protein ID for the highest match.</span></li>
<li style="text-align:justify;"><span style="font-size:11.0pt;font-family:Arial">SignalP: takes a protein sequence as input. The SignalP prediction tool is used to predict the presence of signal peptides in the sequence.</span><span style="font-size:11.0pt;font-family:Arial"> </span></li>
</ol>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: large; "><b><span style="font-family: Arial; ">Biomashup Examples</span></b></span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: medium; "><span class="Apple-style-span">We have created a range of biomashups which are intended as an initial seed of a broader range of components. These biomashups demonstrate the capabilities of the mashup technology and we encourage other groups to develop and share their mashups here. Other mashup examples are also available at: </span></span><span class="Apple-style-span" style="font-size: 15px; "><a href="http://www.mquter.qut.edu.au/bio/biomashups.aspx"><span style="font-size: medium; ">http://www.mquter.qut.edu.au/bio/biomashups.aspx</span></a></span><span style="font-size: medium; "><span class="Apple-style-span">.</span></span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: medium; "><span style="font-family: Arial; ">These mashups may address general tasks:</span></span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: small; ">1. Uniprot - Genbank Id translator: Mapping Uniprot Protein Accession Ids to their GenBank equivalents. Available at: </span><a href="http://www.popfly.com/users/jsum/Uniprot%20to%20Genbank%20X-ref"><span style="font-size: small; ">http://www.popfly.com/users/jsum/Uniprot%20to%20Genbank%20X-ref</span></a><span style="font-size: small; "> <br />
</span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: small; ">2. Genbank to Pubmed Retrieving articles from the Pubmed database that reference a user-specified GenBank Accession Id. Available at: </span><a href="http://www.popfly.com/users/jsum/GeneId%20Article%20Viewer"><span style="font-size: small; ">http://www.popfly.com/users/jsum/GeneId%20Article%20Viewer</span></a></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: medium; ">or more specific tasks. A suite of mashups to perform protein analysis has also been developed. These mashups take a protein in the form of a protein sequence or a Uniprot protein ID and return information about its characteristics, either through retrieval of information from a database or through prediction of structural or functional characteristics. </span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: medium; ">Examples include:</span></p>
<p class="MsoNormal" style="text-align: left; "><span style="font-size: small; ">3. Protein Characteristics Mashup 1: Retrieves known characteristics about a protein from UniProt, OMIM, GO, PRINTS, PROSITE and KEGG databases when a protein ID is provided. Available at: </span><a href="http://www.popfly.com/users/fsn/Protein%20Characteristics%20Mashup%201"><span style="font-size: small; ">http://www.popfly.com/users/fsn/Protein%20Characteristics%20Mashup%201</span></a></p>
<p class="MsoNormal" style="text-align: left; "><span style="font-size: small; ">4. Protein Prediction Mashup 1: Predicts the presence of signal peptides, transmembrane helices, phosphorylation sites, and O-glycosylation sites in a protein sequence. Available </span><a href="http://www.popfly.com/users/fsn/Protein%20Prediction%20Mashup%201"><span style="font-size: small; ">http://www.popfly.com/users/fsn/Protein%20Prediction%20Mashup%201</span></a></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size: medium; "><span class="Apple-style-span" style="font-weight: bold; ">Further information</span></span><span class="Apple-style-span" style="font-size: 15px;"><br />
</span></p>
<p class="MsoNormal" style="text-align: left; "><a style="text-decoration: none;" href="http://www.mquter.qut.edu.au/bio/biomashups.aspx"><span style="font-size: small; "><span class="Apple-style-span" style="color: rgb(0, 0, 0); ">For general information, see:</span></span></a><a href="http://www.mquter.qut.edu.au/bio/biomashups.aspx"><span style="font-size: small; ">http://www.mquter.qut.edu.au/bio/biomashups.aspx</span></a></p>
<p class="MsoNormal" style="text-align: left; "><span style="font-size: small; ">More information about biomashups for protein analysis, including a full list of Popfly Blocks, can be found at: </span><span style="font-size: small; "><span class="Apple-style-span"><a href="http://www.popfly.com/users/fsn/Protein%20Biomashups%20Summary%20page">http://www.popfly.com/users/fsn/Protein%20Biomashups%20Summary%20page</a></span></span><span class="Apple-style-span" style="font-size:15px;"><br />
</span></p>
BioMashups
James M. Hogan
mashups