I am having some fun running AlphaPulldown on a computing cluster. A requirement is to have input sequences in FASTA format. I found that I needed to get ~600 sequences. I had a list of the relevant Uniprot IDs. Surely getting the sequences for these proteins should be straightforward? Solution The Uniprot IDs can be converted – using the ID Mapping Tool on the Uniprot website – into any number of other IDs.
Once again the GigaScience Press team has gathered at the yearly ISMB (Intelligent Systems for Molecular Biology) meeting to find out about the state of the art of computational biology, as well as celebrate our birthday . Hosted this year in the beautiful city of Lyon, and this year collocated with ISMB’s European sibling ECCB, it’s now been 11 years since GigaScience journals launch at ISMB 2012 in Long
It’s DNA day, celebrating two historic milestones: The publication of the structure of DNA in 1953, and the completion of the human genome project in 2003.
The UCSC Xena platform provides an unprecedented resource for public omics data from big projects like The Cancer Genome Atlas (TCGA), however, it is hardfor users to incorporate multiple datasets or data types, integrate the selected data withpopular analysis tools or homebrewed code, and reproduce analysis procedures.
In Sultry Switzerland, Bioinformatics is Radiant at ISMBECCB Water cooling of our datacenter (& friends) Regular readers will know GigaScience originally launched at the 2012 ISMB (Intelligent Systems of Molecular Biology) meeting in Long Beach, and every subsequent year the conference has held a special place in our hearts as the place where we celebrate our birthday (see all the previous write-ups in GigaBlog).
What is restez? R packages for interacting with the National Center for Biotechnology Information (NCBI) have, to-date, depended on API query calls via NCBI’s Entrez.For computational analyses that require the automated look-up of reams of biological sequence data, piecemeal querying via bandwith-limited requests is evidently not ideal.
Sequencers versus the smugglers. CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora), is one of the largest and oldest conservation and sustainable use agreements in existence, and provides a legal framework for protecting endangered plants and animals around the world.
GigaScience is always trying to push the boundaries of how we disseminate reproducible research, and to adapt to the challenges of dealing with experiments become more data-intensive.
Björn Grüning modelling one of our t-shirts. Nowadays, massive amounts of diverse data are generated in biomedical research. To manage it and extract useful information, bioinformatic solutions are needed and software must be developed. The development of a tool should always follow a similar process.
At Disney World infancy ends at 3, or at least that is the age children have to start purchasing tickets. It seemed appropriate to celebrate our 4th birthday there. Or at least at the #ISMB16 Computational Biology meeting that was held this week at the Walt Disney World Resort.