We will update the PLoS journals with the Ambra 0.9.5 release tonight. This release focused on development of the long-awaited PLoS Queue syndication module. Starting in January, PLoS will send article packages directly to PubMed Central at publication time. Article packages are currently sent to PubMed Central the same time as they arrive at PLoS so if any errors are found by the PLoS editorial or production teams, we need to send the fixed article packages back for revision. Sending these article packages at publication time will save a lot of time/effort if any errors are found. This also allows us to automatically send article packages, XML and PDFs to other external repositories in the future. The admin panel and publication workflow were updated for this new syndication service.
It seems that the storm slamming the Bay Area also affected the co-location facility UnitedLayer. A power “glitch” in their building brought down one of their big UPS units. This caused power outage to all of their network equipment. When their routers restarted, they were not serving external traffic. And their backup routers also failed.
Last night (September 15), we updated the PLoS Journals to Ambra 0.9.4. This release culminates a many-sprint development effort and huge data migration to provide per-article usage statistics. The article usage statistics join the other article usage data (citations, bookmarks, blog posts, etc.) to allow users new ways to evaluate the value of articles. Mark Patterson has posted a blog entry about the Article-level Metrics at PLoS. More information about our article-level metrics program can be found in our PLoS FAQ and the Article-level Metrics website.
On May 7 – 8th, I attended the inaugural meeting of the Concept Web Alliance. CWA wants to enable interoperability between large triple stores like the Large Knowledge Collider (LarKC) and provide an Open Access mechanism for accessing the triple stores. This is great for the projects in life sciences as the semantic triple stores are becoming the de facto way to store data for gene expression and sequencing, biobanks, etc.
Yesterday, we migrated
A number of factors contributed to the long outage today. The outage was caused by the sabotaged fiber-optic cable lines San Jose. This affected the network traffic going to United Layer, our co-location facility. United Layer is supposed to have a redundant network line for failover in case something like this happens. I don’t know the details, but this redundant network line wasn’t working. Their engineers finally rerouted their customer’s traffic around the San Jose disruption at 1:43pm PST.
Tonight, we upgraded the PLoS journal websites to Topaz 0.9.2. This release is chock full of user interface changes and enhancements. We’ve completely redesigned the article page to accommodate new features and give a better visual experience to the user. Since this is a significant design change for the article layout, we’d like to hear from our users. Email us or reply to this blog post and let us know what you think about the changes.
At 5pm PST, we will update the PLoS journal websites to Topaz 0.9.1.. The journal websites will be offline for approximately one hour. Once the upgrade is complete, the websites will be a bit slow for the first couple of hours while the caches re-fill. We will run scripts before go-live to re-fill the caches for articles linked from the homepage and the current issue, so the most recent articles should display quickly to the end user.
We had an outage on our PLoS.org domain resources yesterday due to a DNS issue. As a result, www.plos.org and all of the plos.org subdomains were intermittent as well. The issue was addressed promptly but there was a 2-10 hour delay while DNS servers were updated and ~24 hour delay before a comprehensive international DNS update. Most people were able to access www.plos.org within a few hours.
Last night, we upgraded the journal websites to Topaz 0.9 rc1 (rc1 because this is a “beta” 0.9 release). The development for this release focused on performance and stability – specifically to alleviate the sluggish speed of the websites and the pain of ingests.