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News archive

Welcome to the LIMSwiki news archive.

January 3, 2017:

Lab book - Lawrence Berkeley National Laboratory - DSC08822.JPG

2016 had its share of ups and downs for many, and the same holds true for LIMSwiki. From a web attack to dealing with time constraints, it was all about resources, resources, resources. As the wiki has grown over the years, more time has been required for weekly, monthly, quarterly, etc. maintenance tasks. Despite this, however, a few new projects sprung up on the wiki. Though not complete, we made significant headway on a directory (with external links) of U.S. government- and/or self-certified Small Business Administration (SBA) entities offering custom software development and general IT services under government contract. (The idea was those seeking laboratory and scientific informatics implementations could also investigate SBA providers for their service needs.) Developing and adding content for book format was also a goal in 2016, including topics such as medical implants, chemistry, health and biomedical informatics, and web application security, among others. And of course we had smaller updates, such as adding LinkedIn URLs to vendor pages, to go along with long-term maintenance and content addition goals like expanding our open-access journal articles on a weekly basis. Finally, development of a huge education-related project took up a significant portion of the latter part of 2016; details will appear here in the news in the coming month or so.

We hope in 2017 to continue adding useful content while striving to find balance with the increasing number of maintenance tasks. Happy wikiing, and Happy New Year!

Shawn Douglas (talk) 17:43, 3 January 2017 (UTC)

October 12, 2015:

LIMSforum Large.png

The tangentially related LIMSforum — a leading forum on laboratory, medical, and scientific informatics — has moved again due to unfortunate changes by the host LinkedIn. Forum moderator John Jones explained it this way:

"All, it is with regret that I must make the decision to leave Linkedin as the forum for our group. Linkedin has planned changes that will make this group unworkable. We believe strongly in open information and Linkedin is planning changes that would severely disrupt this. However, there is good news... I have planned for this day and knew that Linkedin would pull some sort of bone head idea like this, so I have been working on a complete new site that will let us all carry on our great discussions and a whole lot more. You will be able to login with your Linkedin account and continue as usual."

The forum is now hosted at http://www.limsforum.com/forum/ and can still be used with your LinkedIn ID.

Shawn Douglas (talk) 15:23, 12 October 2015 (UTC)

June 15, 2015:

Sourceforge logo.png

I've been following the antics of open-source hosting site SourceForge for several years now, wanting to give them a chance to turn a sinking ship around with better, more community-friendly tactics. However, it's become clear to me within the last week that the people running the site have fully managed to drive the site off the cliff, never to return to respectability. The site has been packing crappy add-ons and bloatware with select popular software packages for quite some time, but lately the site owners have gone too far. While the need to monetize the site to pay for hosting seems reasonable, the owners of the site have gotten out of hand. (Actually, they don't even pay that much for hosting, if anything, depending on the generosity of others to mirror the site.)

Major projects have been leaving SourceForge in droves, but that hasn't stopped the SourceForge team from doing more harm: they resorted to taking over abandoned accounts and repackaging software with malware, etc. Calls for other projects to leave SourceForge have gotten louder over the past few days, with the team of well-regarded text editor Notepad++ being the latest to leave while encouraging others to do the same.

We've been linking directly to SourceForge pages for most of our open-source software pages, but that will now end. External links to SourceForge on open-source pages will be removed, though a text comment will remain if the project can ONLY be found on SourceForge. It will then be up to the user to decide to visit SourceForge and search for the project there. We do not wish for LIMSwiki users to fall prey to their unfriendly tactics, thus the changes. (Clarification: SourceForge-based citations used to document history will remain, per wiki policy. Only external stand-alone links are being removed.)

Shawn Douglas (talk) 18:24, 15 June 2015 (UTC)

May 18, 2015:

Bratislava New Year Fireworks.jpg

In early May this year we surpassed 1,000,000 page views of LIMSwiki's front page! Sure, that probably mixes in a fair amount of bot indexing and personal updating and reference of the front page, but we're still happy to see that number rise.

I personally started working on the wiki on April 15, 2011, and just over four years later we're still getting plenty of eyes on the site. Admittedly, other projects have taken away some of my time from contributions; however, there's still a boatload of work to be done, from page additions to formatting updates. Like any good wiki, it's always a work in progress. We hope you've all gotten good use out of it and will continue to benefit from new additions as they arrive.

Shawn Douglas (talk) 16:42, 18 May 2015 (UTC)

January 5, 2015:

Faraday-Daniell.PNG
Happy New Year, dear LIMSwiki users! Though every year — let alone every day — is a mixed helping of the good and bad, we hope 2014 brought a few reasons to smile.

The wiki in 2014 was not so much about a few big additions but numerous small additions and changes, which is typical for this kind of publishing format. We continued maintenance, completed a few small projects like making a LIMSWiki:Glossary of the non-vendor content and adding information about the U.S. physician office laboratory. At the end of the year, we also quietly began working on a much more ambitious project that will eventually change how we present vendor software and their publicly known features in a more intuitive way. (We'll give you all more details once we're ready to begin implementing the changes on vendor records.)

2015 will likely bring other additions, including more articles on informatics topics, industries affected by laboratory informatics, etc. Of course, we'll continue to diligently maintain existing content and update it to the best of our ability and resources. As always, if you want to contribute neutral, cited content, you can always request an account.

Have a good 2015, and stick around. There's always more to come here.

Shawn Douglas (talk) 12:53, 5 January 2015 (EST)

August 25, 2014:

Information overload1.jpg
Have you ever experienced information overload? Maybe you were like the person in this image at one point, baffled by too many choices and not enough organization. Yet as society continues its march towards further digitizing and storing content and data, finding exactly the information you want becomes increasingly daunting. Organizing and presenting large amounts of information well is now a desirable trait, whether it's a programmer developing a user interface and query tools for laboratory informatics software or a teacher creating an online course using a learning management program like Moodle.

We've also tried to be cognizant of this problem when determining how to present information in this wiki. The front page has evolved to better and more appealingly organize data access into little "portals" or jumping-off points. But even that becomes increasingly daunting as wiki content continues to be added. This requires a more thoughtful approach using built-in and third-party tools for the wiki software. One recent attempt to organize information involves the use of MediaWiki's category tags to better effect. I personally create 18 broad categories that all or most of our non-vendor wiki content falls under. The results of that effort can be found at the LIMSWiki:Glossary page. Some may find those categorizations too broad; however, articles can have more than one category. I want to use these 18 categories (with the potential for more later) to cover the entire non-vendor article base. Additional category tags can be applied to further granulate those categories, including crossover. For example, electronic data interchange may be categorized under the glossary category "Software and hardware terms" and hospital information system under "Software systems," yet both share the category tag "Health informatics."

Another attempt to organize this wiki's content is via the MediaWiki Collection extension. This allows users to render wiki content into a digital book-like structure. We have a live example with the The Complete Guide to LIMS & Lab Informatics. The upside is a user can learn about a topic from a curated collection of wiki content. The downside is the content is static, meaning like traditional published documents a new copy must be made to contain updated content. However, we've included live links to the contained articles on the wiki page.

As we continue our efforts to add more content, we're hoping tools like the glossary and Collection continue to make approaching the wiki's content less intimidating, alleviating the worries of information overload. We'll also continue to evaluate the front page and how it can be used to better make content easier to find.

Shawn Douglas (talk) 12:53, 25 August 2014 (EDT)

April 30, 2014:

I wanted to highlight some of the projects we've worked on over the past few years. I feel like as the wiki grows, some of the tools buried within it tend to get lost. First, I'd like to again mention the LIMSwiki informatics resource portal. This project was dedicated to collating as many useful online scientific and health informatics-related materials and research tools as possible. It includes links to books, magazines, journals, blogs, organizations, special-interest groups, government entities, academic programs, conferences, trade shows, research tools, job boards, and a whole lot more related to laboratory, health, and other types of informatics. I can't stress enough how extensive we've tried to make this collection of resources.

We have other resources too that shouldn't go unnoticed:

Shawn Douglas (talk) 17:43, 30 April 2014 (EDT)

November 1, 2013:

We have a couple of brief updates to give you regarding the wiki. First, we've expanded the help section of the wiki by updating a few existing help pages and adding a few new ones. Additionally, we've added a new collection of MediaWiki training guides to 1. help users new to MediaWiki more rapidly make meaningful edits and 2. to further encourage new users to make wiki contributions. We hope you find the training guides and exercises useful. Second, we've upgraded to MediaWiki 1.21.2, added new extensions, and will be moving the content to what will hopefully be a more rapid server. All these upgrades should translate to a more functional and inviting informatics wiki. Happy wiki-ing!

Shawn Douglas (talk) 13:42, 1 November 2013 (EDT)

September 04, 2013:

Tycho Brahes stora murkvadrant, Nordisk Familjebok.jpg
After a brief hiatus this summer, we're back in business here on the wiki. As always, maintenance and updates to existing material remain vital. In this rapidly changing world of information technology, advances in products as well as closures by vendors happen frequently. With such a small group of regulars dedicated to maintaining this wiki, there's bound to be information that is out-of-date or inaccurate. We continue our call out for a few good editors to lend a hand with research and updates to our content, whether it be vendor updates or contributions to technical articles. For example, there are many branches of informatics, but little is written about them still.

Please consider requesting a LIMSwiki account if you feel you can contribute neutral, well-researched content to the wiki. And If after reading the guidelines you still need a little help, write a brief message on my talk page, and I'll help how I can. We might even be able to organize an online tutorial together. And many thanks to our contributors!

Shawn Douglas 15:17, 4 September 2013 (EDT)

April 05, 2013:

We've added a few new tools since last year, including expanding the front page to include useful links to existing content. The most recent addition is the LIMSwiki informatics resource portal, a huge collection of web links related to bio, clinical, medical, health, and laboratory informatics (among others). This collection of resources includes books, journals, blogs, web portals, government and academic programs, conferences, trade shows, knowledge bases, research tools, and much more. A link is also added to this front page for easy access. We hope you find it useful.

Shawn Douglas 19:30, 5 April 2013 (EDT)

October 26, 2012:

Quality citations lend reputability to LIMSwiki content and confidence to readers.
For many citations are a necessary evil. I try not to think of them that way. Rather, citations give the written content — whether it's about a LIMS vendor, an open-source software solution, or a piece of laboratory equipment — credibility, and they give readers more confidence in what they're reading.

That said, I want to 1. remind users of the LIMSwiki citation guidelines and 2. offer a little help. I know for beginner wiki editors citations can be daunting. If after reading the guidelines you still need a little help, write a brief message on my talk page, and I'll help how I can. We might even be able to organize an online tutorial together.

Shawn Douglas 13:53, 26 October 2012 (EDT)

April 10, 2012:

The front page has received a facelift. A major complaint of the wiki so far has been that it's not terribly clear where to find the most usable material on the wiki at the moment. We've been so concerned with the content that other aspects have been taken for granted. Hopefully this front page overhaul makes it a bit easier to find the juiciest tidbits. As new material continues to be added, we'll be vigilant and update the front page as necessary.

Shawn Douglas 15:03, 10 April 2012 (EDT)

February 22, 2012:

Thankfully data storage and analysis in the lab has gotten easier.
Yes, this wiki is still alive! It's strange to think it's been almost a year since it was introduced. Since then those with the time to spare have added a wide variety of infrastructure and some content. It has been a slow process, however, and like any major wiki project, more knowledgeable and dedicated editors are needed.

So what has been going on with the wiki? The initial focus was to get some of the major concepts like laboratory information management system (LIMS) and electronic laboratory notebook (ELN) documented at least up to a decent state of quality, with room for article improvement later on. Then a fair amount of effort went into documenting just who is selling LIMS, LIS, ELN, and CDMS. More infrastructure went into place for categories, and a method was put in place for vendors to include a knowledge base on the wiki. Most recently work has been done to track the features LIMS vendors publicly advertise for their LIMS and document them on each vendor page. That work — along with work detailing what each piece of LIMS functionality generally does — is still in progress.

As for the future, we hope to build a critical mass of people willing to help research, write, and cite information about all things laboratory informatics. The need for storing laboratory data, analyzing samples, and improving workflow will only become greater, and with that need comes a demand for clear and referenced information about laboratory data management and the laboratories that require it.

Best,

Shawn Douglas 15:57, 22 February 2012 (EST)

May 22, 2011:

Genomics is only one branch of science that heavily depends on laboratory informatics.
While researching modern vendors of laboratory informatics software, I stumbled across a post by LABVANTAGE's Terry Smallmon from earlier this month. In it he rightfully points out that while the nomenclature of laboratory informatics has historically had distinct subdivisions such as LIMS, ELN, and CDS, times are changing. The lines that differentiate a LIMS from a SDMS, for example, have blurred significantly, almost to the point where the nomenclature is losing its meaning in some cases. Smallmon also notes that as vendors take a more modular approach to laboratory informatics, the distinctions fade even more. Finally he points out that at least for him, determining what a potential customer needs shouldn't be based on nomenclature alone, but rather on the problem(s) a customer is trying to solve.

From my limited perspective, I can't disagree with Smallmon's observations. In fact, the blurred definition of laboratory informatics solutions is referenced in several cases among the major articles. However, I feel it important to emphasize that while definitions of these solutions may be blurring, a rough majority of vendors seem to continue using the nomenclature to describe their offerings. While I can understand the trepidation and skepticism behind trying to more appropriately define the industry nomenclature, the endeavor still seems a worthy one. Sure, we'll never have full agreement on the definition of any one term; however, by making the effort to coalesce the history of laboratory informatics, the industry should in theory have more cohesion.

As an outsider looking in, I perceive this to be a desirable goal. Laboratory informatics is an increasingly vital component of laboratories and scientific research. I recently was told a story from a programmer friend who works in genomics. He related that from his viewpoint, there's an increasingly large bottleneck between the amount of data being created in genomics labs and how it's stored and processed. This really struck home for me. As technology allows for better data collection, so should it allow for better storage and processing. And laboratory informatics is at the center of all of this. Faster and more efficient systems will be needed, and regardless of nomenclature, these solutions will solve problems.

That said, collecting the history and relevant information surrounding the field can only help unify the effort to create better solutions. The names and definitions of those solutions may change with time, but it doesn't mean we shouldn't make the effort. Just as we document the never-ending changes of language in dictionaries, so should we document the changes of the laboratory informatics industry. It's poised to play an important role in humanity's advancement.

Best,

Shawn Douglas 18:43, 22 May 2011 (EDT)

May 18, 2011:

Quick update: most of the work right now is going into the LIMS vendor, LIS vendor, ELN vendor, and other vendor pages. These vendor lists will have limited sort features and include information about vendors past and present. The biggest part of this effort is going towards researching if a particular vendor and/or laboratory informatics program is still active. Sometimes information is lacking to the point where we're unable to determine what happened to a vendor. These instances are being marked with a status of "unknown." The best-case scenario is that current and future wiki users can fill in the blanks where necessary.

Thanks,

Shawn Douglas 20:47, 18 May 2011 (EDT)

May 9, 2011:

We're beginning to close in on a month since the introduction of this wiki, and we're already at 142 articles. While most of them are article stubs, content has been appearing steadily to the wiki. It's the positive contributions of those familiar with laboratory informatics that will assure the continued growth and development of the content here. With a quick grasp of the wiki posting guidelines and how referencing works, anyone familiar with some sort of knowledge of the industry should be able to help with this wiki's content.

Much research and effort has went into important topics like LIMS and ELN, while the articles for LIS and SDMS may require additional relevant material and references. And of course there are plenty of "stub" articles that only have a sentence or two that will need more content. We're working to clean up a vendors page for specific industries and create a template to make it easier for vendors to begin an article about their company. There's also a promised walkthrough of wiki referencing in the works, so stay tuned.

For now please contribute how you can, and if you have questions, contact me on my personal talk page.

Thanks,

Shawn Douglas 17:07, 9 May 2011 (EDT)

April 28, 2011:

Please follow the previously posted title guidelines. The biggest problem is we shouldn't be capitalizing every word in a title unless it's a proper noun. Every article with this error must either be deleted and re-entered anew, or redirected to a new entry. This can take a considerable amount of work to correct.

Another thing to note is that when it comes to internal wiki links, we should only be linking the first instance of a term and not all subsequent instances as well. For example, an article talking about LIMS should only link the first instance, not all instances in the article. Otherwise a page gets very spammy.

Thanks,

Shawn Douglas 21:32, 28 April 2011 (EDT)

April 18, 2011:

For future reference, article titles with words should only have the first word capitalized unless there's a proper name included.

Also, plurals are frowned upon. For example the proposed title "Interface Groups" should be "Interface group" to meet naming conventions. I'm occasionally guilty of forgetting the naming conventions for wiki article titles also, so don't feel bad. Here are the naming conventions, listed from Wikipedia:

  • Use lower case, except for proper names: The initial letter of a title is almost always capitalized; subsequent words in a title are not, unless they are part of a proper name, and so would be capitalized in running text; when this is done, the title will be simple to link to in other articles: Northwestern University offers more graduate work than a typical liberal arts college. For initial lower case letters, as in eBay, see the technical restrictions page. See also the special rules on capitalization in bird naming.
  • To italicize a title, add the template {{italic title}} near the top of the article: Use of italics should more or less conform to these italics guidelines.
  • Use the singular form: Article titles are generally singular in form, e.g. Horse, not Horses. Exceptions include nouns that are always in a plural form in English (e.g. scissors or trousers) and the names of classes of objects (e.g. Arabic numerals or Bantu languages).
  • Avoid abbreviations: Abbreviations and acronyms are generally avoided unless the subject is almost exclusively known by its abbreviation (e.g. NATO and Laser). The abbreviation UK, for United Kingdom, is acceptable for use in disambiguation. It is also unnecessary to include an acronym in addition to the name in a title.
  • Avoid definite and indefinite articles: Do not place definite or indefinite articles (the, a and an) at the beginning of titles unless they are part of a proper name (e.g. The Old Man and the Sea) or will otherwise change the meaning (e.g. The Crown).
  • Use nouns: Titles should be nouns or noun phrases. Adjective and verb forms (e.g. democratic, integrate) should redirect to articles titled with the corresponding noun (Democracy]], Integration), although sometimes they will be disambiguation pages, as at Organic. Sometimes the noun corresponding to a verb will be the gerund (-ing form), as in Swimming.
  • Do not enclose titles in quotes: Article titles which are quotes (or song titles, etc.) are not enclosed in quotation marks (e.g. To be, or not to be is the article title, while "To be, or not to be" is a redirect to that article).
  • Do not use titles suggesting that one article forms part of another: Even if an article is considered subsidiary to another (as where summary style is used), it should be named independently. For example, an article on transportation in Azerbaijan should not be given a name like "Azerbaijan/Transportation" or "Azerbaijan (transportation)" – use Transportation in Azerbaijan. (This does not always apply in non-article namespaces: see Help:Subpage.)

Source: http://en.wikipedia.org/wiki/Wikipedia:Naming_conventions

-Shawn