I have a soft spot for Flybase. My Ph.D. work used Drosophila and I’ve used Drosophila species to teach after that. Something about Dipteran genetics fascinates me. FlyBase is also one of the older genetics and genomics databases and we’ve got a tutorial on it. Today’s tip is their 12 minute video of FlyBase for [...]
NCBI was created in 1988 and has maintained the GenBank database for years. They also provide many computational resources and data retrieval systems for many types of biological data. As such they know all too well how quickly the data that biologists collect has changed and expanded. As uses for various data types have been [...]
Over 2 years ago I did a tip of the week on Phosida (links to Phosida). Phosida is a database of phosphorylation, acetylation, and N-glycosylation data. Since the last tip, Phosida has undergone significant growth and some changes, including the addition of much more data (80,000 phosphorylation, acetylation and N-glycosylated sites from 9 different species) and tools [...]
MycoCosm is a fungal genomics database and browser at JGI, home of a lot of great resources. This week’s tip is from their video tips, which are useful. MycoCosm includes browsers of annotated data of many fungal genomes, KEGG pathway data, synteny data and much more. Their list of video tips include an introduction to [...]
microRNAs have become a rich source of research as they probably have a huge effect on gene expression and disease. The human genome may encode over 1,000 miRNAs that target over half of our genes. They might be implicated in a lot of common diseases (which not yet have been picked up in GWAS studies?). [...]
Mary brought up a paper just recently about what we are missing when data mining papers: Figures and figure legends. Enter the NCBI Image database. This very new database includes over 3 million images that are found in the full-text resources (i.e. PubMed Central) at NCBI. So, I did a search for “drosophila phylogeny” and [...]
Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment… From BioMed Central article alert: BioModels Database: An enhanced, curated and annotated resource for published quantitative [...]
We had a tip last week on converting genome coordinates using Galaxy. This week I’d like to introduce you to the Galaxy interface. This screencast was actually done by one of the developers of Galaxy and is a quick introduction to the interface. We are currently working with Galaxy on a longer introduction to the [...]
Comprehensive tutorials on the ASTD, Entrez Protein, and MMDB databases enable researchers to quickly and effectively use these invaluable variation resources. Seattle, WA September 24, 2008 — OpenHelix today announced the availability of new tutorial suites on the Alternative Splicing and Transcript Diversity (ASTD) database, Entrez Protein and the Molecular Modeling Database (MMDB). ASTD is [...]
Comprehensive tutorials on the model organism databases ZFIN, SGD and PlantGDB and GBrowse, a model organism genome browser, enable researchers to quickly and effectively use these invaluable resources. Seattle, WA September 15, 2008 — OpenHelix today announced the availability of new tutorial suites on several model organism resources including Zebrafish Information Network (ZFIN), Saccharomyces Genome [...]
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