Main Page: Difference between revisions

From HIVE Lab
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
(14 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<div style="border: 1px solid #ccc; padding: 10px; background-color: #f9f9f9; border-radius: 5px; text-align: center">
{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}}
'''Welcome to HIVE WIKI'''
__NOTOC__
<!-- BANNER ACROSS TOP OF PAGE -->
<div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;">
    <div style="margin:0.4em; text-align:center;">
        <div style="font-size:160%; padding:.1em;">Welcome to HIVE Wiki,</div>
        <div style="font-size:100%;">The HIVE Lab group is involved in developing the High-performance Integrated Virtual Environment (HIVE) which is a collaborative project between HIVE group at the CBER Food and Drug Administration (FDA) and Dr. Raja Mazumder's HIVE Lab team at George Washington University (GW). Both groups are coordinating their efforts to integrate various high throughput data analysis tools into the HIVE platform.</div>
<br>
        <div style="font-size:100%;">The [https://www.mediawiki.org/wiki/MediaWiki MediaWiki] for the HIVE project. This wiki system provides complementary information to the [https://hivelab.biochemistry.gwu.edu/ HIVE Lab] and is divided into the following main sections:</div>
    </div>
</div>
</div>


<div style="border: 1px solid #ccc; padding: 10px; background-color: #f9f9f9; border-radius: 5px;">
<div style="clear: both;"></div>
The [https://hivelab.biochemistry.gwu.edu/ HIVE WIKI] provides comprehensive information and resources. Here are some key sections:
 
<div style="clear: both;"><br />
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[Projects]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|Projects}}<br>HIVE team projects fall into two major categories:<br>
1) Developing infrastructure for biomedical data analysis<br>
2) Using that infrastructure to integrate and mine the data for knowledge.<br/>
</div>
    </div>
</div>
</div><div style="clear: both;"><div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[GlyGen Workshops]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">{{main|GlyGen Workshops}}The GlyGen project organizes public workshops to learn more about GlyGen and glycoinformatics. The workshops are organised virtually and in-person. Recordings and material of the workshops are released on the GlyGen YouTube channel and also via the wiki page.
</div>
</div>
    </div>
</div></div><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[GlyGen Internships]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|GlyGen Internships}}The GlyGen project offers internships to undergraduate and graduate students in bioinformatics and in biology/biochemistry. These internships expose students to a wide variety of new concepts in bioinformatics and in biology/biochemistry while working on tasks and projects. The internship enable interns to develop their soft-skills and prepares them for the next stage of their career.
</div>
    </div>
</div></div>


<div style="border: 1px solid #ccc; padding: 10px; background-color: #f9f9f9; border-radius: 5px;">
</div><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
[https://hivelab.biochemistry.gwu.edu/projects Projects]
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
<h3>[[GlyGen Interns]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|GlyGen Internships}}The GlyGen project offers internships to undergraduate and graduate students in bioinformatics and in biology/biochemistry. Please refer to this for Interns FAQ and more information on GW Access and requirements.
</div>
</div>
    </div>
</div></div>


<div style="border: 1px solid #ccc; padding: 10px; background-color: #f9f9f9; border-radius: 5px;">
 
[https://hivelab.biochemistry.gwu.edu/publications Publications]
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[GlyGen portal|GlyGen Portal]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|GlyGen portal}}
The [[GlyGen portal]] is the web interface allowing browser based access to the GlyGen data. The portal supports searching for [[Glycan search|glycans]] and [[Protein search|proteins]], display of detailed [[Glycan details|glycan data]] and [[Protein details|protein data]] as well as export features to save the data to the local system. The portal also provides access to the other resources of the GlyGen project and digital resources such as posters, presentations and videos.
        </div>
    </div>
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[GlyGen data repository|GlyGen Data Repository]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|GlyGen data repository}}GlyGen uses unique processing and integration workflow to retrieve and extract data from various resources. After standardization and harmonization, the high-quality datasets are created. The process of dataset creation is fully documented in BioCompute Objects.These datasets are further processed to create JSON objects and RDF triples that populate MongoDB docstore and Virtuoso triplestore backend databases respectively. The docstore is used by various GlyGen web services while the triplestore is accessed through the GlyGen SPARQL endpoint.
</div>
    </div>
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[Frequently Asked Questions]]</h3>
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|Frequently Asked Questions}}
The FAQ section contains a list of questions asked by users regarding using the portal, API and SPARQL endpoint as well as questions related to the data, data integration and quality control.
        </div>
    </div>
</div>
</div>


<div style="border: 1px solid #ccc; padding: 10px; background-color: #f9f9f9; border-radius: 5px;">
<div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
[https://hivelab.biochemistry.gwu.edu/people People]
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[GlyGen web service API|GlyGen Web Service API]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|GlyGen web service API}}The GlyGen APIs allow programmatic access of the GlyGen data objects for glycans, proteins, and glycoproteins in the MongoDB docstore. The GlyGen APIs have been documented using the Swagger framework (https://swagger.io/). Some of these web services are generic and provide searching, listing and detailed record access functionalities for GlyGen data objects, while others are custom designed to respond to specific biological questions or use cases collected from the user community.  
</div>
</div>
    </div>
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[GlyGen triplestore|GlyGen Triplestore]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|GlyGen triplestore}}The GlyGen knowledgebase uses a Virtuoso triplestore to store GlyGen triples data. The triplestore can be accessed through the GlyGen SPARQL endpoint.
</div>
    </div>
    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
        <h3>[[Glycan structure dictionary|Glycan Structure Dictionary]]</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
{{main|Glycan structure dictionary}}The Glycan Structure Dictionary has been developed as a reference dictionary to provide a standardized list of widely used glycan terms that can help in the curation and mapping of glycan structures described in publications.
</div>
    </div>
</div>
=External links=
;Official
*[https://www.glygen.org/ GlyGen official website]
;Glycan search
*[http://glygen.org/glycan_search.html Glycan search] &mdash; Go to GlyGen website to perform Glycan Search
*[http://glygen.org/glycan_search.html#simple_search Simple search]
*[http://glygen.org/glycan_search.html#advanced_search Advanced search]
*[http://glygen.org/glycan_search.html#tutorial Tutorial] &mdash; Learn how to use simple and advanced searches.
;Protein search
*[http://glygen.org/protein_search.html Protein search] &mdash; Go to GlyGen website to perform Protein Search
*[http://glygen.org/protein_search.html#simple_search Simple search]
*[http://glygen.org/protein_search.html#advanced_search Advanced search]
*[http://glygen.org/protein_search.html#tutorial Tutorial] &mdash; Learn how to use Simple and Advanced searches.


<div style="border: 1px solid #ccc; padding: 10px; background-color: #f9f9f9; border-radius: 5px;">
;Glycoprotein search
'''Resources'''
 
* [https://hivelab.biochemistry.gwu.edu/tools Tools]
*[http://glygen.org/glycoprotein_search.html Glycoprotein search] &mdash; Go to GlyGen website to perform Glycoprotein Search
* [https://hivelab.biochemistry.gwu.edu/datasets Datasets]
*[http://glygen.org/glycoprotein_search.html#simple_search Simple search]
</div>
*[http://glygen.org/glycoprotein_search.html#advanced_search Advanced search]
*[http://glygen.org/glycoprotein_search.html#tutorial Tutorial] &mdash; Learn how to use Simple and Advanced searches.
 
;Quick search
 
*[http://glygen.org/quick_search.html Quick search] &mdash; You can search by glycan, protein, species, and disease.
 
;Try Me
 
*[http://glygen.org/index.html#tryMe Try me] &mdash; To perform search select one of the frequently asked questions.
 
;List pages
 
*[http://glygen.org/glycan_list.html?id=443e99091f8d68ec4da5298ef4bc38fb Glycan list] &mdash; GlyTouCan Accession: G17689DH
*[http://glygen.org/protein_list.html?id=f751fd2a68123d47217597efbf434f67 Protein list] &mdash; UniProtKB Accession: P14210-1
*[http://glygen.org/glycoprotein_list.html?id=f9a835629d7033c218bac73a97ab73d3 Glycoprotein list] &mdash; UniProtKB Accession: P14210-1


<div style="border: 1px solid #ccc; padding: 10px; background-color: #f9f9f9; border-radius: 5px;">
;Detail pages
[https://hivelab.biochemistry.gwu.edu/gallery Gallery]
</div>


<div style="border: 1px solid #ccc; padding: 10px; background-color: #f9f9f9; border-radius: 5px;">
*[http://glygen.org/glycan_detail.html?glytoucan_ac=G17689DH Glycan details] &mdash; GlyTouCan Accession: G17689DH
'''More'''
*[http://glygen.org/protein_detail.html?uniprot_canonical_ac=P14210-1 Protein details] &mdash; UniProtKB Accession: P14210-1
* [https://hivelab.biochemistry.gwu.edu/opportunities Opportunities]
*[http://glygen.org/glycoprotein_detail.html?uniprot_canonical_ac=P14210-1 Glycoprotein details] &mdash; UniProtKB Accession: P14210-1
* [https://hivelab.biochemistry.gwu.edu/events Events]
</div>

Revision as of 17:22, 22 November 2024


Welcome to HIVE Wiki,
The HIVE Lab group is involved in developing the High-performance Integrated Virtual Environment (HIVE) which is a collaborative project between HIVE group at the CBER Food and Drug Administration (FDA) and Dr. Raja Mazumder's HIVE Lab team at George Washington University (GW). Both groups are coordinating their efforts to integrate various high throughput data analysis tools into the HIVE platform.


The MediaWiki for the HIVE project. This wiki system provides complementary information to the HIVE Lab and is divided into the following main sections:

Projects

Template:Main
HIVE team projects fall into two major categories:
1) Developing infrastructure for biomedical data analysis
2) Using that infrastructure to integrate and mine the data for knowledge.

GlyGen Workshops

Template:MainThe GlyGen project organizes public workshops to learn more about GlyGen and glycoinformatics. The workshops are organised virtually and in-person. Recordings and material of the workshops are released on the GlyGen YouTube channel and also via the wiki page.

GlyGen Internships

Template:MainThe GlyGen project offers internships to undergraduate and graduate students in bioinformatics and in biology/biochemistry. These internships expose students to a wide variety of new concepts in bioinformatics and in biology/biochemistry while working on tasks and projects. The internship enable interns to develop their soft-skills and prepares them for the next stage of their career.

GlyGen Interns

Template:MainThe GlyGen project offers internships to undergraduate and graduate students in bioinformatics and in biology/biochemistry. Please refer to this for Interns FAQ and more information on GW Access and requirements.


GlyGen Portal

Template:Main The GlyGen portal is the web interface allowing browser based access to the GlyGen data. The portal supports searching for glycans and proteins, display of detailed glycan data and protein data as well as export features to save the data to the local system. The portal also provides access to the other resources of the GlyGen project and digital resources such as posters, presentations and videos.

GlyGen Data Repository

Template:MainGlyGen uses unique processing and integration workflow to retrieve and extract data from various resources. After standardization and harmonization, the high-quality datasets are created. The process of dataset creation is fully documented in BioCompute Objects.These datasets are further processed to create JSON objects and RDF triples that populate MongoDB docstore and Virtuoso triplestore backend databases respectively. The docstore is used by various GlyGen web services while the triplestore is accessed through the GlyGen SPARQL endpoint.

Frequently Asked Questions

Template:Main The FAQ section contains a list of questions asked by users regarding using the portal, API and SPARQL endpoint as well as questions related to the data, data integration and quality control.

GlyGen Web Service API

Template:MainThe GlyGen APIs allow programmatic access of the GlyGen data objects for glycans, proteins, and glycoproteins in the MongoDB docstore. The GlyGen APIs have been documented using the Swagger framework (https://swagger.io/). Some of these web services are generic and provide searching, listing and detailed record access functionalities for GlyGen data objects, while others are custom designed to respond to specific biological questions or use cases collected from the user community.

GlyGen Triplestore

Template:MainThe GlyGen knowledgebase uses a Virtuoso triplestore to store GlyGen triples data. The triplestore can be accessed through the GlyGen SPARQL endpoint.

Glycan Structure Dictionary

Template:MainThe Glycan Structure Dictionary has been developed as a reference dictionary to provide a standardized list of widely used glycan terms that can help in the curation and mapping of glycan structures described in publications.

External links

Official
Glycan search
Protein search
Glycoprotein search
Quick search
  • Quick search — You can search by glycan, protein, species, and disease.
Try Me
  • Try me — To perform search select one of the frequently asked questions.
List pages
Detail pages
Retrieved from "https://hivelab.biochemistry.gwu.edu/wiki/index.php?title=Main_Page&oldid=128"