All posts (Page 130 of 131)
A guest blog post by Steve Moss
Why Python? A little background!
I started using Python in the summer of 2010. I had applied for the Master of Research postgraduate degree in Computational Biology at the University of York. They teach the programming portion of their course using Python. I thought it might be useful to learn it, before starting, to give me a bit of a head start.
...This is a guest post by Class-Thido Pfaff
We here present the BEFdata R package as part of the rOpenSci project. It is an API package that combines the strengths of the BEFdata portal in handling small, complex datasets with the powerful statics package R. The portal itself is free software as well and can be found here.
The BEFdata platforms support interdisciplinary data sharing and harmonisation of distributed research projects collaborating with each other. They upload, validate and store data from a formatted Excel workbook. Metadata can be downloaded in Ecological Metadata Language (EML) format. BEFdata allows the harmonization of naming conventions by generating category lists from the primary data, which can be reviewed and managed via the Excel workbook or directly on the platform. BEFdata provides a secure environment during on-going analysis; project members can only access primary data from other researchers after the acceptance of a data request The combination allows for efficient storage, description and access of research data. The package leverages the access to datasets as well as to workflows in form of R scripts stored on the portal for provenance tracking of computed results.
...Many US federal agencies are now running app competitions to highlight their web services (see here), and hopefully get people to build cool stuff using government data (see Data.gov for more). See here for a nice list of the US government’s web services.
One of these agencies was the United States Geological Survey (USGS). They opened up an app competition and [we won best overall app! Check out our app called TaxaViewer here: http://glimmer.rstudio.com/ropensci/usgs_app/. We were directed to use one or more of their web services, including mashing up with other web services. Of the USGS web services, we only used ITIS, but included 4 web services from other providers.
...Real use cases from people using our software are awesome. They are important for many reasons: 1) They make the code more useable because we may change code to make the interace and output easier to understand; 2) They may highlight bugs in our code; and 3) They show us what functions users care the most about (if we can assume number of questions equates to use).
If someone has a question, others are likely to have the same, or a similar question. Thus, we are sharing use cases on our blog.
...Scholarly metadata - the meta-information surrounding articles - can be super useful. Although metadata does not contain the full content of articles, it contains a lot of useful information, including title, authors, abstract, URL to the article, etc.
One of the largest sources of metadata is provided via the Open Archives Initiative Protocol for Metadata Harvesting or OAI-PMH. Many publishers, provide their metadata through their own endpoint, and implement the standard OAI-PMH methods: GetRecord, Identify, ListIdentifiers, ListMetadataFormats, ListRecords, and ListSets. Many providers use OAI-PMH, including DataCite, Dryad, and PubMed.
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