As a small team, we don’t have the luxury of dedicated release engineers and thus need to automate our build as much as possible. To do this we use git branches, CruiseControl.rb and some nifty shell scripts to keep new code flowing. Coupled with the automation, we also have a weekly build master rotation where one member of the dev team shields the rest from tracking down build failures.

Ok, a picture is worth a thousand words so here’s our code flow (everything green is automated):

Developers will typically workout out of the DEVELOPMENT branch so this is where new code begins flowing through the system. We find that it’s good practice to link submissions to GitHub issues for management & deploy tracking. The changes then get pulled intoSTAGING which is the continuous build branch for automated testing. We like CruiseControl.rb because it’s light weight & low maintenance. If tests fail, the build master is notified and he can track down the right person to fix the failing test in staging. Once the build is green, the qualified code gets pushed to MASTER which is the production branch behind pubget.com. Since the master branch is considered the healthiest, it feeds down into development and any other project branches that may exist. At this point every branch now has that latest code change and the process begins again.

Too many words? Here’s the short flow:
  1. devs submit to development
  2. changes are tested in staging
  3. qualified changes get pushed to master
  4. development & special project branches stay close to shore through master
It’s definitely worth mentioning that when test failures happen in staging, the automation pauses. Nothing is pulled from development into staging and nothing is pushed from staging into master. This ensures that only healthy code makes its way into production and only the developer that broke the build needs to fix staging. Other developers can continue merging changes into development knowing they will be tested once staging is working again.

This process has helped in a bunch of ways:
  • developers submit code and trust that it will be qualified, deployed & propagated to all branches
  • developers stay productive even when the build is broken
  • we have a production branch where we can quickly apply a hotfix if needed

We here at Pubget know how much serious work is involved in obtaining your PhD but as we have found out humor is just as big of a process! In any case, we’re pumped to be sponsoring UCSF’s PhD film series this Thursday.

With all the time our research friends are saving by searching on Pubget, they can afford to take a well-deserved break from some intense research.

Free pizza and some laughs, what could be better?

Well you can read our official stance below, but here’s the short of it. 

As the search engine for life science PDFs, we want to index scientific works from journals that have a strong impact on the scientific community. The journals indexed publish papers which represent the advancements in science, and are the foundation of future discoveries. That’s why you’ll find both the latest issues of your favorite life science journals, as well as papers that represent the foundation of scientific thinking. 

Here’s our official stance: 

Pubget carefully evaluates and selects content which meets the highest standards of scholarly research from varied disciplines and geographic locations. Journals included in Pubget are examined for timeliness, originality and impact of research, and quality of editorial work. Journals included inPubget contain various article formats from literature review to original research and contain mostly unsolicited works and some commissioned works. The journal’s peer review process is stated clearly with an appropriate percentage of accepted manuscripts and require authors to declare ethical concerns and conflicts related to published works. Many journals publish works reporting on nationally or federally funded research and provide a strong contribution to the field.

Journals with articles that are 100% commissioned, contain less than 3 articles per volume, authored works by editorial board members,advertisement connecting articles, or reprints of previously published works are not included in Pubget.



We hope we’re able to strike a balance between covering everything that the scientific research community needs, while maintaining a high quality of search results. In fitting with our goal, we are actively expanding our index to include important research for the life sciences and beyond. Are their journals that you wish we indexed? Tell us in the comments or write to us at team(at)pubget(dot)com.

don’t know how many of you heard the news out of Princeton last week. And no, I’m not talking about its US News ranking (although go Tigers). I’m talking about the news that the university will ask its scientists to publish only in open access journals. The impetus was apparently to make sure faculty can send around copies of papers they publish without fear of running afoul of a publisher’s copyright.


The event is the latest in a trend toward open access that began in earnest several years ago, when the U.S. government mandated that all research paid for by taxpayer dollars—-through grants from the National Institutes of Health, for example—-be available to those taxpayers free of charge. A compromise was struck with publishers, whose business models largely depend on charging for data, whereby papers would still cost money to access for a certain period immediately after publication before being deposited in a free government-run repository thereafter. Prominent universities like Yale and Harvard have also undertaken open-access policies. As a result, some traditionally subscription-only publishers now allow authors to designate that papers be open-access from the outset, for a fee.

As you can imagine, we follow these things rather closely at Pubget, because they have a direct impact on how we get you papers. Pubget is already the fastest way to get you PDFs that are open access (we help you get your subscription PDFs faster, too, if you’re at one of our 400+ institutions). But knowing when a paper’s become open access takes a bit of work—-and not just for us, but for publishers themselves: because traditionally papers have either been subscription or open access from the start, a world in which different papers in the same journal could potentially be either taxes traditional infrastructure that was built from a journal’s eye view, if you will.

At Pubget, we look at things the way you do: paper by paper. We’ve been working directly with publishers to help them realize our common mission: of letting you get the information you need to do amazing things. But meanwhile, what the news out of Princeton really got me thinking was how much I want to thank all of you out there who have been writing us whenever they find open-access papers that have fallen through the cracks. So, thank you for helping us help you do science at speed.

How many coffees does it take to make Pubget?
About 50 business days ago we got a new coffee machine. It has a neat feature that it actually counts all the coffees it makes. The number today was 1483. This means, it takes about 30 coffees a day!

How many coffees does it take to make Pubget?

About 50 business days ago we got a new coffee machine. It has a neat feature that it actually counts all the coffees it makes. The number today was 1483. This means, it takes about 30 coffees a day!

The now famous, Big Bang Theory inspired remake of the Flash inspired t-shirts have arrived at Pubget.

The now famous, Big Bang Theory inspired remake of the Flash inspired t-shirts have arrived at Pubget.

Big news! Our iPad app is now available to download from the App Store. You can get it here(for free).

The app combines our streamlined paper access technology with the iPad’s portability. Use the app just like pubget.com to find and save your papers. Unlike other apps on the market, you do NOT need to build a library of papers first, because it comes preloaded with 30 million science papers that you can access with your library’s subscriptions.

It’s important to mention that the Pubget for iPad app was made possible by our collaboration with Sigma Life Science to develop the app’s concept and bring it to you. Learn more here.

App Features:

  • Search everything in PubMed, ArXiv, JSTOR, IEEE and more
  • Access your library’s subscriptions: it’s synced with 450 libraries world-wide (and growing!)
  • Immediately get the full text PDF through your library
  • View PDFs inline (no link-outs or dead-ends)
  • Save papers offline
  • Type and save notes for specific papers
  • Search complex queries with Advanced Search

Happy Searching!

I heard the coolest thing the other day, so cool I had to sit down. 

Terry Gross was interviewing Charles Mann on NPR’s Fresh Air. Mann has just written a book called “1493” about the ecological aftermath of Columbus’ discovery. I’d learned a little about this in school: how Europeans introduced horses, how tomatoes come from the Americas. But I’d never heard that before Columbus, northern North America had no earthworms. They’d been wiped out there by the last Ice Age, says Mann. And so the leaves that fall here in New England would pile up into mats that trees would grow straight out of. Today earthworms turn those leaves into soil. If you spent any time in the woods as a kid, the thought of no earthworms and the ground under your feet having been totally different might have the same effect on you as it did on me. 

The story goes that the worms came in soil in the ballast of ships sent to bring tobacco back from Virginia to Europe (tobacco being another American original). In the centuries since, says Mann, a “worm front” has been spreading out from the eastern seaboard. Today it has reached as far as Minnesota, where the Minnesota Worm Watch is deputizing the locals to try to save the native forest. Needless to say I want to read this book. Very cool. 

The story got me thinking: what makes something cool? What is it about a book or story or research paper that makes you stop and say “wow” and want to tell people about it? And being practical, can one define a set of metrics or attributes that we can use to keep ourselves in a steady supply of cool? 

To be cool something has to be interesting, of course, but also new and unexpected. Connecting otherwise unrelated things—-electrodes and cooking hot dogs; the Santa Maria and a 5,000-mile inexorable front of earthworms—-seems also to be important. Mixing scales of measure—-the very big and very small, or the very quick and very slow—-also helps. But are all new, unexpected connections between unrelated things at different scales of measure cool? Do these things explain what makes this paper cool? 

What makes a paper cool to you?

“The future is already here—-it’s just not very evenly distributed.”

So goes the old saying by William F. Gibson, sci-fi noir visionary and author of the cult classic Neuromancer. He’s right, of course. And you don’t have to stray too far from Pubget to see it.

I work at one of the greatest hospitals in the world, a 600-bed tertiary care center in Boston. It’s on the cutting edge of medical technology. And yet, like cutting-edge hospitals everywhere, many of its countless computers and the software they run are not cutting edge at all: small screens, old software.

There are good reasons for this, reasons that chief information officers at any large organization struggle with all the time. One is the expense of updating hardware and software; another is reliability, especially at places where decisions are literally life and death. The result is a tension between the need to maintain a working status quo and the desire to update in order to leverage new technologies that can make an organization go faster—-technologies like Pubget.

Our users tell us how amazing it is to type in a search on Pubget and get the PDF right away. But it’s easy to take for granted all the pieces that have to be in place to make Pubget work. Your computer has to have a modern browser (sorry, Internet Explorer 5 and 6). Your browser has to be able to display any PDF inline (ahem, Google Chrome on Mac). When these things aren’t in place, you have to have the know-how and access privileges to download or install new software. And of course your processor and internet connection have to be fast enough to let you do all these things at speed.

The truth is, while a lot of us take these things for granted, many of us just don’t have them. The future is here, it’s just not very evenly distributed.

Large organizations tend to update many of their computers all at once, but they don’t do this often. Between updates, browsers and plugins improve, but users are often prevented from installing them. This prevents chaos inside the organization and makes it easier for IT staff to diagnose and resolve problems to keep it running smoothly. But what if you’re one of the many people who work at one of these organizations and still want the benefit of PDFs right away? What if you know the future’s here and want your share?

As we’ve grown here at Pubget we’ve been thinking a lot about people like you, and we’ve been working on a solution. Over the summer we’ll be rolling out some changes to Pubget.com that should make it easier to get PDFs fast no matter where you are or what computer setup you have. You’ll still be able to use the site as you see it today. But we hope you’ll find the new changes useful.

We also hope you’ll tell us what you think! The future may be unevenly distributed, but with your help we can do our best to get you there.

A picture is worth a thousand words. At Pubget we’re always talking about all the papers you can read on the site, especially if you’re at an activated institution. (Being “activated” means your school or workplace works with Pubget so we can give you all your journal subscriptions.) Our focus on papers is part of how we make science faster for you.

But clicking through this week’s New England Journal of Medicine—-I have it set as one of my favorite journals, so the latest issue is only ever a click away from the Pubget home page—-reminded me of another cool thing about getting PDFs right away: you get to see the figures right away, too.

Take Images in Clinical Medicine, one of the coolest features of the NEJM. Each week, Images in Clinical Medicine describes a medical finding in pictures, captioned with a paragraph about how the patient presented and what the finding means. These pictures are dramatic, arresting, sometimes shocking. A leg and foot that are mottled pink and yellow due to cholesterol emboli. A threadlike white worm growing in an eye. Blackened, charred-looking fingers due to a blood viscosity problem. These are only a few of the many interesting cases the NEJM has covered in recent years.

Checking out the latest Images in Clinical Medicine was one of our favorite things to do each week back in med school. We would have spent hours just flipping through them, if there had been a way to do that, but there wasn’t. With Pubget, there is. With this one search, you can flip through the last 10 years’ worth of Images in Clinical Medicine (assuming, of course, that you’re at an institution that subscribes to the NEJM). Check it out—-it’s a absolute blast.

Publishers have made great leaps forward with how they display articles online. It’s been especially nice to see how some folks, including PubMedCentral, give you thumbnails of images that you can click to enlarge. But for many of my peers in research and at the hospital, there’s just no substitute for having figures there at full size—-especially for Images in Clinical Medicine—-especially when you’re flipping through the paper for the first time. A lot of us read
papers by first flipping through the figures. Publishers do such a nice job on their print layouts that it’s a shame to miss out on that experience, just because you want the speed associated with getting things online. That’s why we’ve done what we’ve done at Pubget: so you can see the figures, as well as the paper, as fast as possible. Because a picture is worth a thousand words.

Use Zotero? You can now open any saved citation in your Zotero library as a PDF via Pubget

First, make sure you have downloaded the latest version of Zotero. You can get it hereTo learn more about Zotero, click here to go to their instructions page.

Directions

To open citations from your Zotero library as PDFs via Pubget, follow these quick steps:

1. Click on the Zotero icon in the bottom right of your internet browser.

2. Select the locate arrow icon, then select Manage Lookup Engines.

3. The Article Lookup Engine Manager window will open. You will see that CrossRef is already setup as a default.

4. Select Toggle, to activate the Pubget Article Lookup (you will see a check mark appear next to Pubget Article Lookup). If you are using a PC, you will need to select OK.

You can close this window now: you’re all set up.

Zotero Setup

From here on, you can easily open your Zotero citations as PDFs via Pubget.

1. Just highlight the citation you want in your Zotero library, then select the locate arrow icon.

2. Select Pubget Lookup from the drop-down menu, and the PDF will automatically open in Pubget. 


Zotero Lookup

Just a quick post this time, as we’re busy around the office preparing some amazing new things that we’ll be unveiling this summer.

Ray Kurzweil, who has two papers in Pubget, was in the news again about a month ago. He’s the futurist author of books about the Singularity, the time when scientific progress happens faster than the human brain can keep up with it. At Pubget, which is all about science at speed, the Singularity comes up in conversation from time to time. But I realized I’d never actually sat down and read about it. Where’s the idea come from? Should we believe it? And of course, in a humbler way, how does Pubget fit in?

So I picked up Kurzweil’s “The Singularity Is Near.” (Actually, I downloaded it on my iPhone. iBooks is my Angry Birds.) And here’s what I learned. Take out a pen and paper and write down a list of breakthroughs in human invention and discovery. The wheel. Electricity. The internal combustion engine. Things like that. Then write down the earliest known date for each breakthrough. (This might require some trips to Wikipedia.) What you’ll notice, says Kurzweil, is things are happening faster: breakthroughs are happening more and more closely together. In fact, if you plot each breakthrough on a graph, where the axes are when it happened and the time since the last breakthrough, you’ll find that breakthroughs fall on a curve. (It’s a little like Moore’s Law.) And if you trace that curve forward into the not-too-distant future, it says breakthroughs as important as the wheel will start happening every minute, then every second, then—-for all intents and purposes—- instantaneously. You can think of the time when that starts happening as the Singularity.

It’s a pretty far-out idea, and it raises some questions. How good is the data on the timing of these breakthroughs? What constitutes a breakthrough, anyway? Isn’t there an inherent recall bias, where you’re more likely to remember things that happened more recently, making it look like things are happening faster when actually they aren’t? And even if they are, can a trend like this really go on forever? I won’t give anything away, but the book deals with a lot of these questions. At the end of the day, one thing’s for sure: if breakthroughs are indeed happening faster and faster, it’s not under the direction of any one person or group. It’s the result of billions of people doing what they’ve been doing since time immemorial: solving problems, making things better, faster. It’s only when you step back to consider the whole sweep of history that it fits a pattern. Here at Pubget, we’re just trying to make science faster for you. The next paper you read, the next one you write, know that you are part of the same grand tradition of moving things forward—-if Kurzweil’s right, faster than ever before.

At Pubget, we know how important scientific literature is. We even refer to it as the currency of the scientific community. Further, we like to think of ourselves as being ahead of the curve when it comes to changes in how scientific literature is accessed. If you’re an avid Pubget user, you know that goal is to make it easier to find and access scientific literature (that you have legal access to, of course). Apparently, we’re not the only ones who think we’re trendsetters.

Pubget President, Ryan Jones, has been asked to speak on a panel, alongside Reprints Desk, at the Buying and Selling eContent conference in Scottsdale, AZ this year. If you’re at the conference, stop by for what is sure to be an exciting discussion. If you’re not, stay tuned for an update from the talk.

Executive Forum — Models & Modalities

Accessing and Pricing the Scientific Literature

Ryan Jones, President, Pubget
Scott Ahlberg, Head of Corporate Services, Reprints Desk

Access, acquisition, and utilization of published scientific articles is a key activity in R&D, customer support, educational awareness, and promotion of pharmaceutical and healthcare products. Most companies spend well over $1M per year in accessing this type of peer-reviewed content. Ryan Jones of Pubget discusses the varying dynamics of different access models to content, with observations from the cutting edge of content access. Scott Ahlberg of Reprints Desk shares his analysis of article and content pricing, from traditional subscription to document delivery, and reuse licensing options. The presentation concludes with a look at traditional pricing theories and explores how they apply to article pricing and how they differ — all of which ultimately impacts content consumption.

Cambridge, MA, March 8, 2011- Pier Professional announced today that its 15 year journal article archive is now fully searchable with Pubget.

Pubget makes scientific research easier by simplifying the process of finding, managing and analyzing scientific papers. Pubget’s core solution, at Pubget.com, provides article-level tools making content discovery, access and copyright management much easier for the user. As a standalone article destination, Pubget delivers millions of PDF articles from thousands of publishers in one interface.

“We’re constantly looking for new search channels that will allow us to get our content directly into the hands of global users,” said Paul Somerville, Pier Professional’s Marketing and Business Development Manager. “Pubget is an innovative and growing search service that enables academics, students and other users to get to our content seamlessly.”

“Pubget’s mission is to make finding articles faster and easier for researchers everywhere. We’re tremendously excited to add Pier Professional’s journal content to our search service at Pubget.com,” said Ryan Jones, Pubget’s President. “With the addition of Pier Professional’s 23 titles, Pubget’s users will enjoy expanded searchable content, and Pier Professional will gain the exposure to the millions of searches Pubget processes each month.”

The main benefit of this service enables subscribing institutions to get direct access to Pier Professional’s full-text articles with Pubget— eliminating many of the hurdles typical of research today. For other non-subscribing institutions, users are directed to purchase PDF articles via Reprints Desk (reprintsdesk.com) or directly from the Pier Professional website.

“We hope that by increasing discoverability and ease of use for users to get to our content, will lead to more increased usage and engagement with existing and new, global customers,” said Paul Somerville.

Want to see how Pubget works? Click on the following link to watch Pubget’s demo:http://goo.gl/zj6Iv

About Pier Professional:
Pier Professional (previously known as Pavilion Journals) has over 20 years of publishing experience and working in partnership with leading experts in health and social care and academia across the public, private and not-for-profit sectors.

Pier Professional strives to disseminate innovation and best practice across the health and social care field. There are currently huge changes taking place in the field; integrated working, individualised care, quality, the ageing population to name but a few. Pier Professional aims to ensure that the information that it publishes can assist in the learning and development needed at this crucial time of change in both health and social care.

Each journal uniquely bridges the gap between research and practice, creating an arena where researchers, practitioners, academics, professionals and service users can exchange current ideas and learn from evidence-based material. All journals particularly focus on disseminating good practice and highlight clear implications for practice. The journals are edited by leading experts in their field, supported by its publishing team and prestigious editorial boards comprising researchers, practitioners, policy-makers, users and carers.

Pier Professional publishes in association with a range of prominent academic, research, policy and practice partners.

About Pubget:
Pubget makes scientific research easier by simplifying the process of finding, managing and analyzing scientific papers. Pubget’s core solution, at Pubget.com, provides article-level tools making content discovery, access and copyright management much easier for the user. Pubget’s corporate services offer relevant banner and contextual advertisement for marketers and search tools for libraries and R&D departments, including repository and text mining platforms.

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