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<div style="font-size:290%; padding:.1em; text-align: center;">Welcome to the HIVE Lab (Mazumder Research Group) Wiki</div><br>
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        <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 the CBER Food and Drug Administration (FDA) and Dr. Raja Mazumder's team at The George Washington University (GW). This effort aims to integrate various high throughput data analysis tools into the HIVE platform.
         <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>
In addition to the HIVE platform, the group is involved in developing standards for bioinformatics communication via BioCompute Objects, knowledgebases for glycoinformatics (GlyGen), cancer research (BiomarkerKB, OncoMX, BioMuta, BioXpress), and microbiome analysis via the GutFeeling Knowledge Base (GFKB). The lab leverages knowledge graphs and advanced ML/AI technologies, including large language models, to harmonize, map, and uncover valuable insights from clinical data, omics datasets, knowledgebases, and scientific publications.</div><br>
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         <div style="font-size:100%;">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 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>
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         <h3>[[Projects]]</h3>
         <h3>[[Projects]]</h3>
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{{main|Projects}}<br>HIVE team projects fall into two major categories:<br>
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Projects]]''<br>HIVE team projects fall into two major categories:<br>
1) Developing infrastructure for biomedical data analysis<br>
1) Developing infrastructure for biomedical data analysis.<br>
2) Using that infrastructure to integrate and mine the data for knowledge.<br/>
2) Using that infrastructure to integrate and mine the data for knowledge.<br />
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        <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.
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         <h3>[[GlyGen Internships]]</h3>
         <h3>[[Publications]]</h3>
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{{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.
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Publications]]''<br>The HIVE team has a variety of peer-reviewed publications, book chapters, posters, brochures, and multimedia available for the public.<br />
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<h3>[[GlyGen Interns]]</h3>
        <h3>[[People]]</h3>
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{{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.
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[People]]''<br>This page contains details about the HIVE Lab team.<br />
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         <h3>[[GlyGen portal|GlyGen Portal]]</h3>
         <h3>[[Tool Resources]]</h3>
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{{main|GlyGen portal}}
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Tool Resources]]''<br>There are a variety of bioinformatic tool resources developed by our team.
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.  
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         <h3>[[GlyGen data repository|GlyGen Data Repository]]</h3>
         <h3>[[Dataset Resources]]</h3>
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{{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.
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Dataset Resources]]''<br>There are a variety of bioinformatic dataset resources integrated by our team.
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{{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.
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         <h3>[[GlyGen web service API|GlyGen Web Service API]]</h3>
         <h3>[[Opportunities]]</h3>
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{{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.
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Opportunities]]''<br>Interested in joining our team? Learn about our team.
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         <h3>[[GlyGen triplestore|GlyGen Triplestore]]</h3>
         <h3>[[Gallery]]</h3>
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{{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.
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Gallery]]''<br>Interested in joining our team? Learn about our team.
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        <h3>[[Glycan structure dictionary|Glycan Structure Dictionary]]</h3>
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{{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.
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;Official
;Official


*[https://www.glygen.org/ GlyGen official website]
*[https://hivelab.biochemistry.gwu.edu/ HIVE Lab 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.
 
;Glycoprotein search
 
*[http://glygen.org/glycoprotein_search.html Glycoprotein search] &mdash; Go to GlyGen website to perform Glycoprotein Search
*[http://glygen.org/glycoprotein_search.html#simple_search Simple search]
*[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
 
;Detail pages
 
*[http://glygen.org/glycan_detail.html?glytoucan_ac=G17689DH Glycan details] &mdash; GlyTouCan Accession: G17689DH
*[http://glygen.org/protein_detail.html?uniprot_canonical_ac=P14210-1 Protein details] &mdash; UniProtKB Accession: P14210-1
*[http://glygen.org/glycoprotein_detail.html?uniprot_canonical_ac=P14210-1 Glycoprotein details] &mdash; UniProtKB Accession: P14210-1

Revision as of 23:14, 25 November 2024


Welcome to the HIVE Lab (Mazumder Research Group) Wiki
The HIVE Lab group is involved in developing the High-performance Integrated Virtual Environment (HIVE) which is a collaborative project between the CBER Food and Drug Administration (FDA) and Dr. Raja Mazumder's team at The George Washington University (GW). This effort aims to integrate various high throughput data analysis tools into the HIVE platform. In addition to the HIVE platform, the group is involved in developing standards for bioinformatics communication via BioCompute Objects, knowledgebases for glycoinformatics (GlyGen), cancer research (BiomarkerKB, OncoMX, BioMuta, BioXpress), and microbiome analysis via the GutFeeling Knowledge Base (GFKB). The lab leverages knowledge graphs and advanced ML/AI technologies, including large language models, to harmonize, map, and uncover valuable insights from clinical data, omics datasets, knowledgebases, and scientific publications.

This wiki system provides complementary information to the HIVE Lab and is divided into the following main sections:

Projects

    Main article: Projects
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.

Publications

    Main article: Publications
The HIVE team has a variety of peer-reviewed publications, book chapters, posters, brochures, and multimedia available for the public.

People

    Main article: People
This page contains details about the HIVE Lab team.

Tool Resources

    Main article: Tool Resources
There are a variety of bioinformatic tool resources developed by our team.

Dataset Resources

    Main article: Dataset Resources
There are a variety of bioinformatic dataset resources integrated by our team.

Opportunities

    Main article: Opportunities
Interested in joining our team? Learn about our team.

Gallery

    Main article: Gallery
Interested in joining our team? Learn about our team.

External links

Official
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