Lanyrd, the Social Conference Directory

24 11 2010

I’m a blogger who usually needs quite some time to write blog posts. However, I just learned about a new tool that I need not describe in detail. Firstly, because Heidi Allen just described the tool in a blog post here. Secondly, because the tool is so intuitive and easy.

I’m talking about Lanyrd, a directory of geeky events, technical conferences and social meetings.

It is really so simple and effective. Please follow me.

You go to http://lanyrd.com/, connect via OAuth to Twitter and before you can count to 3, Lanyrd shows you the conferences your friends on Twitter are going to as a speaker (blue border) or an attendee. You can also see friends who keep track of the conference (vague).

Unfortunately purely scientific or medical conferences are not included, but who knows what Lanyrd is up to.

You can track the conferences by subscribing in iCal / Outlook. It is also easy to add conferences.

I might go to Medicine 2.0, but I didn’t make up my mind yet. If I click on the link I see the following page:

You can click on “Attend” or on “Track” if this applies. Furthermore you get an overview of the conference: the location, the link to the website, the Twitter account, the hashtag used in tweets (#med2) and of the speakers.

Oh …. there are none yet, so I added a few.

It is easy to do, people who have never logged into the site can also be added. However, if helps to know the exact twitter name, if many people on Twitter share the same name (else you have to check all the profiles generated with Twitter search).

Lanyrd is the baby of the recently married couple Simon Willison and Natalie Downe. And as it goes with babies, they grow up.

What can we expect the next few years?

Simon in the Guardian:

“We have lots of exciting plans for Lanyrd’s future. One of the things we’re very keen on is gathering information on past conferences – speaker slides, videos, audio recordings and write-ups. In five years’ time, we hope we’ll have the best collection of conference coverage possible.”

Credits to Heidi Allen (@dreamingspires) and Anne Marie Cunningham (@amcunningham) who discussed Lanyrd on Twitter. As said, Heidi wrote a post on Lanyrd, and Anne Marie wrote a short blogpost at Wishful Thinking in Medical Education on the need to find list of upcoming medical or health conferences- and the hashtags that would be used to cover them on twitter. The Solution as it appeared was Lanyrd (at least for some of the conferences).





Problems with Disappearing Set Numbers in PubMed’s Clinical Queries

18 10 2010

In some upcoming posts I will address various problems related to the changing interfaces of bibliographic databases.

We, librarians and end users, are overwhelmed by a flood of so-called upgrades, which often fail to bring the improvements that were promised….. or which go hand-in-hand with temporary glitches.

Christina of Christina’s Lis Rant even made rundown of the new interfaces of last summer. Although she didn’t include OVID MEDLINE/EMBASE, the Cochrane Library and Reference manager in her list, the total number of changed interfaces reached 22 !

As a matter of fact, the Cochrane Library was suffering some outages yesterday, to repair some bugs. So I will postpone my coverage of the Cochrane bugs a little.

And OVID send out a notice last week: This week Ovid will be deploying a software release of the OvidSPplatform that will add new functionality and address improvements to some existing functionality.”

In this post I will confine myself to the PubMed Clinical Queries. According to Christina PubMed changes “were a bit ago”, but PubMed continuously tweaks  its interface, often without paying much attention to its effects.

Back in July, I already covered that the redesign of the PubMed Clinical Queries was no improvement for people who wanted to do more than a quick and dirty search.

It was no longer possible to enter a set number in the Clinical Queries search bar. Thus it wasn’t possible to set up a search in PubMed first and to then enter the final set number in the Clinical Queries. This bug was repaired promptly.

From then on, the set number could be entered again in the clinical queries.

However, one bug was replaced by another: next, search numbers were disappearing from the search history.

I will use the example I used before: I want to know if spironolactone reduces hirsutism in women with PCOS, and if it works better than cyproterone acetate.

Since little is published about this topic,  I only search for  hirsutism and spironolactone. These terms  map correctly with  MeSH terms. In the MeSH database I also see (under “see also”) that spironolactone belongs to the aldosterone antagonists, so I broaden spironolactone (#2) with “Aldosterone antagonists”[pharmacological Action] using “OR” (set #7). My last set (#8) consists of #1 (hirsutism) AND #7 (#2 OR #6)

Next I go to the Clinical Queries in the Advanced Search and enter #8. (now possible again).

I change the Therapy Filter from “broad”  to “narrow”, because the broad filter gives too much noise.

In the clinical queries you see only the first five results.

Apparently even the clinical queries are now designed to just take a quick look at the most recent results, but of course, that is NOT what we are trying to achieve when we search for (the best) evidence.

To see all results for the narrow therapy filter I have to go back to the Clinical Queries again and click on see all (27) [5]

A bit of a long way about. But it gets longer…


The 27 hits, that result from combining the Narrow therapy filter with my search #8 appears. This is set #9.
Note it is a lower number than set #11 (search + systematic review filter).

Meanwhile set #9 has disappeared from my history.

This is a nuisance if I want to use this set further or if I want to give an overview of my search, i.e. for a presentation.

There are several tricks by which this flaw can be overcome. But they are all cumbersome.

1. Just add set number (#11 in this case, which is the last search (#8) + 3 more) to the search history (you have to remember the search set number though).

This is the set number remembered by the system. As you see in the history, you “miss” certain sets. #3 to #5 are for instance are searches you performed in the MeSH-database, which show up in the History of the MeSH database, but not in PubMed’s history.

The Clinical query set number is still there, but it doesn’t show either. Apparently the 3 clinical query-subsets yield a separate set number, whether the search is truly performed or not. In this case  #11 for (#8) AND systematic[sb], #9 for (#8) AND (Therapy/Narrow[filter]). And #10 for (#8) AND the medical genetics filter.

In this way you have all results in your history. It isn’t immediately clear, however, what these sets represent.

2. Use the commands rather than going to the clinical queries.

Thus type in the search bar: #8 AND systematic[sb]

And then: #8 AND (Therapy/Narrow[filter])

It is easiest to keep all filters in Word/Notepad and copy/paste each time you need the filter

3. Add clinical queries as filters to your personal NCBI account so that the filters show up each time you do a search in PubMed. This post describes how to do it.

Anyway these remain just tricks to try to make something right that is wrong.

Furthermore it makes it more difficult to explain the usefulness of the clinical queries to doctors and medical students. Explaining option 3 takes too long in a short course, option 1 seems illogical and 2 is hard to remember.

Thus we want to keep the set numbers in the history, at least.

A while ago Dieuwke Brand notified the NLM of this problem.

Only recently she received an answer saying that:

we are aware of the continuing problem.  The problem remains on our programmers’ list of items to investigate.  Unfortunately, because this problem appears to be limited to very few users, it has been listed as a low priority.

Only after a second Dutch medical librarian confirmed the problem to the NLM, saying it not only affects one or two librarians, but all the students we teach (~1000-2000 students/university/yearly), they realized that it was a more widespread problem than Dieuwke Brand’s personal problem. Now the problem has a higher priority.

Where is the time that a problem was taken for what it was? As another librarian sighed: Apparently something is only a problem if many people complain about it.

Now I know this (I regarded Dieuwke as a delegate of all Dutch Clinical Librarians), I realize that I have to “complain” myself, each time I and/or my colleagues encounter a problem.

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Reclaim your Privacy on Facebook using a Simple Bookmarklet

20 05 2010

Of all social networking sites, Facebook causes the greatest privacy concerns. Certainly since it has changed its privacy options over time.

In the beginning, Facebook restricted the visibility of a user’s personal information to just their friends and their “network”, but the default privacy settings have become much more permissive, as you can see in the video below.
This short video is based on a visualization made by Matt McKeon and gives only an impression of a work-in-progress
(for up to date info check the original animation at http://mattmckeon.com/facebook-privacy/).

The reason? According Facebook founder Mark Zuckerberg the controversial new default and permanent settings just reflect the way the world has changed, becoming more public and less private (see ReadWriteWeb).

“Default” is the key to the problems. You have to opt out to protect your privacy. However to fully protect your privacy on Facebook, you have to navigate through 50 settings with more than 170 options (see great charts at the NY Times!). Facebook’s privacy policy is longer than the American constitution!!!

Shocked by the results of the ACLU’s Facebook Quiz (see Mashable), I already changed my privacy settings last summer. Doing a simple quiz on Facebook meant everything on your profile (whether you use privacy settings or not), is available to the quiz. Even more worrying, when your friends do a quiz, everything on your profile is made available to the developers as well.

Since the default privacy settings have changed, my settings needed to be adapted again. But where were the leaks in the 170 options?

Luckily there is a very simple bookmarklet Reclaim Privacy that can check and fix your profile in 2 minutes (see Mashable.com) It is very easy.

1. First go to Reclaim Privacy and drag the bookmarklet to your web browser bookmarks bar
(in the example I dragged the bookmarklet into Chrome’s bookmarks (upper arrow)

2. Go to your Facebook privacy settings and then click that bookmark (Scan for Privacy, see arrow) once you are on Facebook.

3. You will see a series of privacy scans that inspect your privacy settings and warn you about settings that might be unexpectedly public.
In my case my friends could still accidentally share my personal information. This is indicated by a red sign: “insecure.

4. So I clicked “prevent friends from sharing your data”, and in seconds this was the result:

5. I tweaked the contact information a bit (caution) by changing my contact settings, but I still would allow everyone to add me as a friend (I still have to approve, don’t I?)

Piece of cake!





Packrati.us = Twitter + Delicious = Useful + Simple

18 03 2010

To me, Twitter is an essential source for information. It is an easy way to keep updated in my field, it is fast and it is an ideal networking site to build relationships. Without it I wouldn’t have ‘met’ so many excellent and interesting people. In fact those people are my living filter to the Twitter noise (see previous post): I only follow people with whom I share the same interest (at least in some respects). Twitter also is one of my inspirational sources for blogging, and vice versa it is an outlet for my blog posts.

Unfortunately, Twitter has one shortcoming: Tweets are volatile. Twitter is designed to catch conversations real time. Therefore it is not easy to “keep” Tweets or read them later. Usually your tweets get lost after 7 to 10 days and cease to be found by  Twitter Search. Some tweets can still be Googled, but that is not a secure way of keeping tweets.

At least I safeguard my favorited tweets by taking a RSS to my favs (yellow starred in Fig).

But this is just a way to conserve your favorite tweets for a (more) prolonged time.

What you also would like is to “archive” the URLs of the actual pages that seem interesting (the red http links in the tweets).

I used Google Notebook for that. That was near perfect: the free online Google application allowed saving and organizing clips of information (via a Firefox add-on) while online (see Wikipedia). The information was saved to “notebooks” that could be made “public” and automatically fed into Twitter to share with others. It was easy tracing articles back by searching or browsing.

But that is no more. Google decided to drop the development of Google Notebook. In addition, several of of my notebooks  were flagged as violating Program Policies?!

I tried Evernote as an alternative, but it could never win my heart. Too time-consuming, for one thing.

I may not have tried hard enough, but testing tools is not my job. I ‘m just looking for tools/ways that make my live in the web 2.0 world easy. The tools must be easy to understand and easy to use.

A new tool Packrati.us. (http://packrati.us/) seems to meet all my needs in this respect. A week ago, I read about it in a Tech Crunch paper entitled:  Packrati.us: A Dead Simple Way To Make Delicious Bookmark The Links You Tweet. Dead simple that was what I needed!

Packrati.us is a simple bookmarking service. Once you register, they follow your Twitter feed, and whenever one of your tweets contains URLs, they are added to your Delicious.com bookmarks.

So, for instance I retweeted @amcunningham and @jrbtrip, who link to an interesting article regarding bias in dissemination & publication of research. The link is a shortened URL.

When I visit My Delicious (http://delicious.com/) via an add-on in Firefox, I see that the link is automatically saved in Delicious.

The bookmark shows

  1. the link to the URL (title),
  2. the number of people bookmarking the link,
  3. the actual tweet mentioned in notes (more notes can be added),
  4. the extended url,
  5. an automatic tag (packrati.us) chosen to indicate that this bookmark is automatically imported from Twitter and other tags that I manually added to facilitate retrieval.

When you click on the link you go to the actual article. I can always find the bookmark when I search for tags like bias

The following links can be automatically loaded into Delicious:

  • Links in your tweets and retweets (tweets you resend)
  • Links in tweets directed to you (send by others)
  • Links in your favorited tweets (!) (quite new)

You can choose to:

  • Expand the URLs that have been shortened with an URL shortening service
  • Replace existing bookmarks (no duplication, old tags are kept.
  • Not convert hashtags from tweets to tags for the bookmarks (default = tagging hashtags)
  • Exclude tweets with specific tags (new)
  • Exlude tweets from a selection of sources
  • Add the sender of the tweet (other than yourself)

Packrati.us is under continuous development, some features have just been added. I love the new feature that favorited tweets can be kept (alas it doesn’t work retrospectively, so the above favs are not included).

In practice you can get a lot of bookmarks if you tweet/favorite a lot. It is good to exclude some tweets beforehand and imo necessary to prune the tweets afterwards and add tags. Otherwise it becomes a (disorderly) mess.

Although Packrati.us links only Twitter and Delicious, you can use each platform separately. I also use Delicious to manually add bookmarks of websites I like. Yes, thanks to Packrati.us I learned to love delicious again.





#SillySaturday #17 – Social Media Stats per Second

13 02 2010
more about “Garys Social Media Count“, posted with vodpod

Some time ago I saw the above Real Time Social Media Stats Counter at Heidi Allen Online (see here), the blog of Heidi Allen. The live stats meter is actually from Gary Hayes at Personalize Media (see post: Garys Social Media Count).

You can find the embed code at Gary Hayes post. I used the above Vodpod video, because WordPress won’t allow flash.

Yesterday, I saw a similar stats counter (in Dutch) at the excellent Dutch Education Blog  Trendmatcher tussen ICT en Onderwijs (see here) of @trendmatcher (Willem Karrsenberg). Willem saw these real time stats presented in a powerpoint presentation by Toine Maes, director of  “Kennisnet” (~”Knowledge network”). Later he asked Toine how he managed to get these dynamic stats in his slide. Of course it is great to show such a slide in a class room, or at other occasions.

At his blog Willem explains what it takes to make a slide with real life counters yourself. You need the Cortona 3D viewer (download here), that can be embedded in a browser or in Powerpoint. And you need the definition file with the actual formulas.  He made an example of a presentation and has made all files public (download here).

For people (like me) who find this all too complicated he made a simple one minute Flickr-video (FF) you can use instead. I converted this again to a Vodpod video, which easily picks up the embed code (Add-on in FireFox) and can be directly imported into WordPress.

Willem  notes that he doesn’t know if the actual figures are correct. Bas Jonkers of Kennislink commented that the numbers are based on recent data, mostly from indirect sources. With the Cortona 3D viewer you can see the updated data here

Gary Hayes at Personalize Media shares his sources at his blog. The dates are less recent because his post dates from September 2009, but he will update the data from time to time.

For instance:

  • 20 hours of video uploaded every minute onto YouTube (source YouTube blog Aug 09)
  • Facebook 600k new members per day, and photos, videos per month, 700mill & 4 mill respectively (source Inside Facebook Feb 09)
  • Twitter 18 million new users per year & 4 million tweets sent daily (source TechCrunch Apr 09)
  • 900 000 blogs posts put up every day (source Technorati State of the Blogosphere 2008)
  • UPDATE: YouTube 1Billion watched per day SMH (2009)- counter updated!
  • Flickr has 73 million visitors a month who upload 700 million photos (source Yahoo Mar 09)
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When more is less: Truncation, Stemming and Pluralization in the Cochrane Library

5 01 2010

I’m on two mail lists of the Cochrane Collaboration, one is the TSC -list (TSC=Trials Search Coordinator) and the other the IRMG-list. IMRG stands for Information Retrieval Methods Group (of the Cochrane). Sometimes, difficult search problems are posted on the list. It is challenging to try to find the solutions. I can’t remember that a solution was not found.

A while ago a member of the list was puzzled why he got the following retrieval result from the Cochrane Library:

ID Search Hits
#1 (breast near tumour* ) ….. 254
#2 (breast near tumour) …… 640
#3 (breast near tumor*) ….. 428
#4 (breast near tumor) …… 640

where near = adjacent (thus breast should be just before tumour) and the asterisk * is the truncation symbol.  At the end of the word an asterisk is used for all terms that begin with that basic word root. Thus tumour* should find: tumours and tumour and thus broaden the search.

The results are odd, because #2 (without truncation) gives more hits than #1 (with truncation), and the same is true for #4 versus #3. One would expect truncation to give more results. What could be the reason behind it?

I suspected the problem had to do with the truncation. I searched for breast and tumour with or without truncation (#1 to #4) and only tumour* gave odd results: tumour* gave much less results than tumour. (to exclude that it had to do with the fields being searched I only searched the fields ti (title), ab (abstract) and kw (keywords))

Records found with tumour, not with tumour*, contained the word tumor (not shown). Thus tumour automatically searches for tumor (and vice versa). This process is called stemming.

According to the Help-function of the Cochrane Library:

Stemming: The stemming feature within the search allows words with small spelling variants to be matched. The term tumor will also match tumour.

In addition, as I realized later, the Cochrane has pluralization and singularization features.

Pluralization and singularization matches Pluralized forms of words also match singular versions, and vice versa. The term drugs will find both drug and drugs. To match either just the singular or plural form of a terms, use an exact match search and include the word in quotation marks.

Indeed (tumor* OR tumour*) (or shortly tumo*r*) retrieves a little more than tumor OR tumour: words like tumoral, tumorous, tumorectomy. Not particularly useful, although it might not be disadvantagous when used adjacent to breast, as this will filter most noise.

tumor spelling variants searched in the title (ti) only: it doesn't matter how you spell tumor (#8, #9, #10,#11), as long as you don't truncate (while using a single variant)

Thus stemming, pluralization and singularization only work without truncation. In case of truncation you should add the spelling variants yourselves if case stemming/pluralization takes place. This is useful if you’re interested in other word variants that are not automatically accounted for.

Put it another way: knowing that stemming and pluralization takes place you can simply search for the single or plural form, American or English spelling. So breast near tumor (or simply breast tumor) would have been o.k. This is the reason why these features were introduced in the first way. ;)

By the way, truncation and stemming (but not pluralization) are also features in PubMed. And this can give similar and other problems. But this will be dealt with in another blogpost.

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Adding Methodological Filters to MyNCBI

26 11 2009

Idea: Arnold Leenders
Text: “Laika”

Methodological Search Filters can help to narrow down a search by enriching for studies with a certain study design or methodology. PubMed has build-in methodological filters, the so called Clinical Queries for domains (like therapy and diagnosis) and for evidence based papers (like theSystematic Review subset” in Pubmed). These searches are often useful to quickly find evidence on a topic or to perform a CAT (Critical Appraised Topic). More exhaustive searches require broader  filters not incorporated in PubMed. (See Search Filters. 1. An Introduction.).

The Redesign of PubMed has made it more difficult to apply Clinical Queries after a search has been optimized. You can still go directly to the clinical queries (on the front page) and fill in some terms, but we rather advise to build the strategy first, check the terms and combine your search with filters afterwards.

Suppose you would like to find out whether spironolactone effectively reduces hirsutism in a female with PCOS (see 10+ 1 Pubmed Tips for Residents and their Instructors, Tip 9). You first check that the main concepts hirsutism and spironactone are o.k. (i.e. they map automatically with the correct MeSH). Applying the clinical queries at this stage would require you to scroll down the page each time you use them.

Instead you can use filters in My NCBI for that purpose. My NCBI is your (free) personal space for saving searches, results, PubMed preferences, for creating automatic email alerts and for creating Search Filters.
The My NCBI-option is at the upper right of the PubMed page. You first have to create a free account.

To activate or create filters, go to [1] My NCBI and click on [2] Search Filters.

Since our purpose is to make filters for PubMed, choose [3] PubMed from the list of NCBI-databases.

Under Frequently Requested Filters you find the most popular Limit options. You can choose any of the optional filters for future use. This works faster than searching for the appropriate limit each time. You can for instance use the filter for humans to exclude animals studies.

The Filters we are going to use are under “Browse Filters”, Subcategory Properties….

….. under Clinical Queries (Domains, i.e. therapy) and Subsets (Systematic Review Filters)

You can choose any filter you like. I choose the Systematic Review Filter (under Subsets) and the Therapy/Narrow Filter under  Clinical Queries.

In addition you can add custom filters. For instance you might want to add a sensitive Cochrane RCT filter, if you perform broad searches. Click Custom Filters, give the filter a name and copy/paste the search string you want to use as filter.

Control via “Run Filter” if the Filter works (the number of hits are shown) and SAVE the filter.

Next you have to activate the filters you want to use. Note there is a limit of five 15 filters (including custom filters) that can be selected and listed in My Filters. [edited: July 5th, hattip Tanya Feddern-Bekcan]

Under  My Filters you now see the Filters you have chosen or created.

From now on I can use these filters to limit my search. So lets go to my original search in “Advanced Search”. Unfiltered, search #3 (hirsutism  AND spironolactone) has 197 hits.

When you click on the number of hits you arrive at the results page.
At the right are the filters with the number of results of your search combined with these filters (between brackets).

When you click at the Systematic Reviews link you see the 11 results, most of them very relevant. Filters (except the Custom Filters) can be appended to the search (and thus saved) by clicking the yellow + button.

Each time you do a search (and you’re logged in into My NCBI)  the filtered results are automatically shown at the right.

Clinical Queries zijn vaak handig als je evidence zoekt of een CAT (Critical Appraised Topic) maakt. In de nieuwe versie van PubMed zijn de Clinical Queries echter moeilijker te vinden. Daarom is het handig om bepaalde ‘Clinical Queries’ op te nemen in ‘My NCBI’. Deze queries bevinden zich onder Browse Filters (mogelijkheid onder Search Filters)

Het is ook mogelijk speciale zoekfilters te creëeren, zoals b.v. het Cochrane highly sensitive filter voor RCT’s. Dit kan onder Custom Filters.

Controleer wel via ‘Run Filter” of het filter werkt en sla het daarna op.

Daarna moet je het filter nog activeren door het hokje aan te vinken. Dus je zou alle filters van de ‘Clinical study category’ kunnen opnemen en deze afhankelijk van het domein van de vraag kunnen activeren.

Zo heb je altijd alle filters bij de hand. De resultaten worden automatisch getoond (aan de rechterkant).

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