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(1, 'Databases', 'databases', 'databases', 'databases', '\r\n
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Column 1
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Column 2
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GlycobioInformatics Databases
\r\nList of some selected databases that are often used for glycobioinformatics analysis. (see:
Publication)\r\n
CAZy
\r\n
Carbohydrate Active EnZyme database. More information is available in the cazy Web site (see: CAZy)
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GlycoGeneDB (GGDB)
\r\n
Glyco enzyme database. More information is available in the Web site (see: GGDB)
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GlycoEpitope
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On Glycan Binding Proteins. Also available at (see: GlyCosmos.) (see: GlycEpitope)
\r\n
Other Useful Tools
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BRENDA
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A Comprehensive Enzyme Information system. BRENDA also provides structure-based search function.
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RHEA
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It is an expert-curated knowledgebase of chemical and transport reactions of biological interest. (see: RHEA)
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UNIPROT
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It is the world’s leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information. See: UniProt.
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\r\n
About Glycomics Workbench
\r\n
The development of Glycomics Workbench is based on a combination of Grid technology and cloud computing that will be supported by High-Performance Computing (similar technology was used earlier for CHOIS (CHOIS) and various Large Language Models (LLMs) of generative AI for searching and generating chat or text based output. This is designed to serve the Glyco-Community and other researchers who have interest in Glycobiology. Unlike the central dogma where the information or code flows from DNA to RNA to Protein, Glycocode or the code that deciphers the information (human glycocode consists of a combination of 10 monosaccharides in different orders) for a variety of cellular functions including cell signaling are the result of orchestrated functions of a set of glycosyltransferases. A single protein can be decorated by a variety of carbohydrates (syn. Glycans) resulting in multiple forms of glycoproteins. Thus, while the total number of mammalian cellular proteins is estimated at about 20000, glycosylation turns those into unaccounted numbers. Structural identification of those glycoconjugates is time consuming and tedious. Glycome or the carbohydrate (glycan) related data generated using a variety of analytical techniques are needed for their structural identification. A variety of software tools and databases have been developed for Glycomics or the analysis of those glycoconjugates from glycoproteins, glycolipids and proteoglycans (see here for article 16). Not all are web-based making those stand-alone software tools unavailable for use when needed by the Glyco-Community. Glycomics Workbench is designed to provide those tools via C-Grid (see this paper), a community data grid that can be utilized by the developers and researchers for sharing those tools via this web portal. Moreover, this website will serve as a portal providing access to all the web-based resources needed for Glycome research. This is also designed to provide information generated by various LLMs that can benefit the students and researchers learning glycobiology. Educators will also benefit from that information teaching glycobiology in a class-based or one-on-one set-up.
\r\n
GlycobioInformatics Tools\r\n
List of commonly used specialized software tools for Mass Spectral (MS/MS/LC-MS) Data Analysis (see: Publication)
\r\n
BIONIC
\r\n
For Glycopeptide identification, a Proprietary software (see: PMID: 23255153)
\r\n
CARTOONIST
\r\n
For MS analysis of glycan structure, a standalone tool software (see: Yu, CY., et. al., 2013)
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GAGfinder
\r\n
MS analysis specifically for GAGs, A standalone softwar (see: PMID: 29615495)
\r\n
GAG-ID
\r\n
MS analysis of heparin/heparan sulfate, a standalone software (see: PMID: 25887393)
\r\n
GLYCOFOREST
\r\n
LC-MS analysis of glycan, a standalone tool (see: Glycoforest 1.0)
\r\n
GLYCOFRAGMENT
\r\n
For MS analysis of glycan A part of glycosciences.de portal (see: Ref)
\r\n
GLYCOANALYZER
\r\n
Automated glycan annotation software from MS analysis data, a standalone software (see: PMID: 22903841)
\r\n
Other Useful Tools
\r\n
GRITS Toolbox
\r\n
A platform for glycomics data processing and archiving.
\r\n
GlycobioInformatics Portals
\r\nList of portals that are commonly used for glycobioinformatics analysis. (see: Publication)
\r\nGlycomics@ExPaSy
\r\nGateway to multiple resources, part of SIB resources; also includes GlyConnect. (see: Expasy)
\r\nGlyCosmos
\r\nGlycome database Supported by JSCR (see: GlyCosmos)
\r\nOther Useful Tools
\r\nProtein Data Bank (PDB)
\r\nA PDB A single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
', '2024-05-07 06:16:09', '2024-05-07 06:16:36', NULL, 'sidebar-left'),
(5, 'Info Links', 'Glycomics Workbench', 'Glycomics Workbench', 'info-links', 'The federal government Office of the National Coordinator for Health Information Technology (ONC) is at the forefront of the administration’s health IT efforts and is a resource to the entire health system to support the adoption of health information technology and the promotion of nationwide health information exchange to improve health care. ONC is organizationally located within the Office of the Secretary for the U.S. Department of Health and Human Services (HHS).
\r\nThe National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services (HHS), is the primary Federal agency for conducting and supporting medical research. It also provides authentic health information for public awareness (see; also see, AHRQ). Its Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), established by U.S. congress in 1962, conducts and supports research on topics related to the health of children. To learn more about the Institute and its activities, see.
\r\nCenters for Disease Control and Prevention (CDC) is dedicated to protecting health and promoting quality of life through appropriate information on the prevention and control of disease. Also, see its National Center for Public Health Informatics (NCPHI).
\r\nThe Lawrence Gartner, M.D., FAAP and Carol Gartner, Ph.D. Pediatric History Center is dedicated to preserving and cataloguing materials representing the history of pediatrics and children\'s health care. It also serves as the repository of the Archives of the American Academy of Pediatrics (AAP).
\r\nThe American Medical Association (AMA) guides medical professionals helping patients by uniting physicians nationwide to work on important professional and public health issues.
\r\nThe Center for Nutrition Policy and Promotion at the United States Department of Agriculture (CNPP) is dedicated to improve the health and well-being of Americans by developing and promoting dietary guidance that links scientific research to the nutrition needs of consumers. To learn more about the Center and its activities, see.
\r\nWhen Kenneth H. Cooper, M.D., M.P.H., published his first bestseller, Aerobics, in 1968, he introduced a new word and a new concept in US. Millions of americans started exercising, motivated by his preventive medicine research, persuasive public appearances, and a series of inspiring books. In short, it started a fitness revolution. He then founded The Cooper Institute in 1970, to promote fitness education in US and across the Globe. To learn more about the Institute and its activities, see.
', '2024-05-07 06:18:20', '2024-05-07 06:18:20', NULL, 'sidebar-left'),
(6, 'home', 'Glycomics Workbench', 'Glycomics Workbench', 'home', '\r\n
\r\n
News & Views
\r\n
\r\n![\"](\"images/NIHlogo.jpg\")
\r\nNIH announced new strategic plan Bridge2AI. Find out more here on the strategic plan for Bridge2AI research.
\r\n- \r\n
NIH announced new programs under Common Fund. Bridge2AI here Bridge2AI is a short-term, goal-driven strategic investment supported by the NIH Common Fund. See its recent announcements: SysBio (https://commonfund.nih.gov/venture/sysbio) and Occulomics (https://commonfund.nih.gov/venture/oculomics).
\r\n \r\n
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Welcome Message
\r\n
In collaboration with the glyco-community, higher education, and industriesDCG is engaged in developing software tools and technologies that can benefit this field of study.
\r\n
\r\n
\r\n
Education & Training
\r\n
Educating the workforce with proper training particularly on the application of CI-supported tools for glycome research is an important activity of DCG. Read here for more.
\r\n
\r\n
test
', 'http://glycomicsworkbench.org/dev/', 'yes', '2024-05-05 13:23:26', '2024-05-07 10:42:10'),
(4, 'Glycoproteins', 'Glycomics', 'About Glycoproteins', 'uploads/sliders/1714937094.jpg', 'uploads/sliders/t1714937094.jpg', 'Carbohydrates are often covalently bonded to the side chains of amino acids in proteins forming glycoproteins. This attachment, termed glycosylation, can occur either at the nitrogen atom in the side chain of asparagine (N-linked glycosylation) or at the oxygen atom in the side chain of serine or threonine (O-linked glycosylation) of the amino acids. Glycosylation can occur either during protein translation or as a post-translational
', 'http://glycomicsworkbench.org/dev/', 'yes', '2024-05-05 13:54:55', '2024-05-05 13:54:55'),
(5, 'Glycolipids', 'Glycomics', 'About Glycolipids', 'uploads/sliders/1714937135.jpg', 'uploads/sliders/t1714937135.jpg', 'Carbohydrates when bind to a lipid via a glycosidic bond form glycolipids. The lipid portion can be either a glycerolipid (with a glycerol backbone) or a sphingolipid (with a sphingosine backbone). Fatty acids are connected to this backbone, resulting in a polar head and a non-polar tail. The carbohydrates attached to the polar head groups on the cell\'s outer surface form the ligand components of glycolipids. These are
', 'http://glycomicsworkbench.org/dev/', 'yes', '2024-05-05 13:55:35', '2024-05-05 13:55:35'),
(6, 'Proteoglycans', 'Glycomics', 'About Proteoglycans', 'uploads/sliders/1714937199.jpg', 'uploads/sliders/t1714937199.jpg', 'Proteoglycans are macromolecules consisting of a core protein to which one or more glycosaminoglycan (GAG) chains are covalently attached. The core protein can be either a glycerolipid or a sphingolipid. The GAG chains are long, linear carbohydrate polymers with negative charges due to sulfate and uronic acid groups. The point of attachment is typically a serine (Ser) residue, forming a tetrasaccharide bridge. These are found in our bodies, particularly in connective tissues, bone, cartilage, and cell surfaces.
', 'http://glycomicsworkbench.org/dev/', 'yes', '2024-05-05 13:56:39', '2024-05-05 13:56:39'),
(7, 'Roles in Health & Diseases', 'Glycomics', 'Health & Diseases', 'uploads/sliders/1714938778.jpg', 'uploads/sliders/t1714938778.jpg', '\r\n
\r\n
You need to use Laravel Eloquent feature to make timestamps written to the Database automatically, when you insert data directly, Laravel does not know about your timestamps. You need to set the timestamps manually in the insert statement.
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