LIMS on the internet: the LIMS mailing list

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internet column LIMS on the lnternet: the LIMS Mailing List Stu Miller

Sudbury, Ontario, Canada This article describes the laboratory information management system (LIMS) Mailing List, the topics which are acceptable for discussion on the list, how users can subscribe to the list and interact with the software that manages list traffic. 1. Introduction: what is a LIMS? Most analytical chemists will be familiar with the concept of a laboratory information management system (or LIMS for short) in some form or another. A LIMS defined in its simplest form is"the system a laboratory uses to manage its data and disperse the results to designated areas" [ 1].(LIMS are not only used in analytical laboratories but are also common in industrial plants and pharmaceutical operations. However, to simplify things I will continue to refer to organizations utilizing LIMS as 'labs' in the rest of this article.) In the area of data management, LIMS are many things to many people. The system a lab uses to manage its data may be as simple as a paper filing system of handwritten forms or as elaborate as a client/server relational database management system (RDBMS) w,tilizing the latest in wireless network and pen computing technologies.

The computerized LIMS may be as simple as one desktop computer used to 'login' samples and manually enter data in a spreadsheet-like interface with plain text reports of results given to clients. It may be also be as complex as: • a fleet of roving pen computers 'wired' to a wireless local area network (LAN) and used by analysts to enter data at the bench-top, instantly transferring the data to a database server • 'live' instrument interfacing • personnel and resource management • complete accounting and invoicing • consumable supply inventory management • sample archiving In the complex computerized LIMS data dispersal may include: • colour graphical reports and images • automated electronic data reporting via e-mail or fax • fax on demand • customer files downloaded from file transfer protocol (FTP) sites or bulletin board system (BBS) file services • even event-triggered data transfer to corporate systems such as accounting or computerized manufacturing systems Although it would be a bit much to ask all this of a single system, all the 'parts' mentioned above exist in a functioning LIMS somewhere and this description illustrates the level of power (and complexity) that these systems are capable of delivering.

2. The need for a LIMS resource After making the decision to implement a LIMS, a lab may choose to develop its own system 'inhouse' using existing resources or to buy one of the existing commercial LIMS products. As you may gather from the descriptions above, expecta~ tions can be very lofty and anyone venturing into purchasing or designing a LIMS for the first time will find a dizzying array of products and technologies which may need to be employed to satisfy user demands from the system. 0165-9936/96/$15.00 P I I S0165-9936 (96) 00008-8

© 1996 Elsevier Science B.V. All rights reserved

trends in analytical chemistry, vol. 15, no. 4, 1996

Not only does implementing a new system present great challenges but administrators of existing LIMS are also faced with the challenges of maintaining and customizing their systems, whether they be in-house or commercial, to live up to the expectations of users and management. Given the diverse knowledge required to specify, implement and maintain a modern LIMS there is an obvious need for a vendor-independent LIMS-resource where management, users and administrators can discuss issues of interest or trade information pertinent to all stages of system implementation with other LIMS users. However, even with the apparent explosion of information available on the Internet within the last year, until recently there were no resources available to the LIMS user or administrator on the Internet. Searching on the Internet in both Gopher-space and the World Wide Web ( W W W ) on the word 'LIMS' produces a few 'hits' on sites of commercial vendors se'~ing or supporting their products but little else. The LIMS Mailing List was created to provide a vendor-independent forum for discussing topics of interest to LIMS users and administrators of commercial or in-house LIMS products. This article, will present a description of the L,IMS Mailing List and how it may serve users and ~:~dministrators of both commercial and in-house systems.

3. Internet discussion forums: why a mailing list? The idea for creating the LIMS List came about as an alternative to a small LIMS e-mail 'discussion group' of about 12 users that was started about a year ago by the author. At the time, there were no known Usenet newsgroups dealing specifically with LIMS. The first attempts at establishing a vendor-independent LIMS newsgroup suffered from a lack of support from interested, potential users. Instead, a mailing list was established and announced in a few trade journals such as American Laboratory [ 2] and a LIMS newsletter called the LIMS/Letter [ 3 ] as well as at the !995 International LIMS Conference [4 ] in Bonn, Germany. Response to the list has been excellent with the number of subscribers recently passing the 600 mark. For those not familiar with mailing lists, a program called a 'list server' is used to receive, manipulate, store and send all mail that is sent to a list.

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E-mail sent to the list is routed in and out of the list server allowing it to process the message appropriately. Mailing lists can provide most of the same functions as a newsgroup without the need for access to a news reader or a news feed from a service provider. Posts to the lists are archived in a compressed format and can be easily retrieved by subscribers of the list at any time by sending a simple e-mail message to the list server. For those concerned about filling up their mailboxes, the list also supports a 'digested' mode where all messages from the day's list activity are compiled, indexed and sent in a single message to the subscriber (see Fig. 3). 3.1. Goals of the list and subject matter suitable for discussion on the list

The goals of this mailing list and guidelines for content appropriate for discussion are contained in the list charter, parts of which are tabulated below. 1. The LIMS Mailing List provides a vendor-independent forum for discussing topics and issues related to LIMS. Subject matter appropriate to this mailing list includes, but should not be limited to: • LIMS reference sources o LIMS product research • LIMS needs analysis • LIMS procurement • database specific issues with LIMS • hardware/operating system specific issues with LIMS • configuration/installation specific issues with LIMS • design and functionality issues with LIMS • quality control/quality assurance issues with LIMS e regulatory compliance issues with LIMS • data security/verification/integrity etc. 2. The list also provides a vendor-independent forum for sharing ideas or methods for LIMS development, installation and/or maintenance with an aim to improving users' own LIMS in their organizations. 3. The list provides a vendor-independent forum for announcing professional meetings of interest to LIMS users. 4. The list will also promote awareness and information about LIMS. Note: advertisements for products marketed for commercial gain may not be distributed v~a this mailing list. Failure to comply will result in all

trends in analytical chemistry, vol. 15, no. 4, 1996

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To subscribe to the LIMS Mailing List send an e-mail message to

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subsequent messages from the sender to be ignored by the list server. However, all LIMS developers or vendors are encouraged to post questions and comments about LIMS as well as to actively respond to questions and criticisms of their products in relation to a given discussion. 3.2. How to subscribe to the list

Subscribing to the mailing list is simple and f~ee. You may subscribe to the mailing list by sending an e-mail message to the list server as described below (see Fig. 1). Subscribers unfamiliar with Internet mailing list 'etiquette' should note that 'administrative' requests (i.e. requests to subscribe, unsubscribe, request list info or archived files) should only be sent to the [email protected] address. All list mail you want other subscribers to read should be sent to the [email protected] address. Termlnll - MNDM.TRM

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(replace 'yourfullname' with your own name) as the first and only line in the body of the message (subject lines are ignored by the list server). The list server will take your e-mail address from the header of your message and put you on the list. You will receive an acknowledgment message shortly with a welcome message and instructions on how to interact with listproc to send basic messages. Once you have received a message confirming you are subscribed, you can send messages to all other subscribers of the list by sending a message to

[email protected] Any inquiries regarding the list can be addressed to Stu Miller ([email protected]). Note: there are known problems with the ListProcessor software and certain 'X400' and 'EPO' mail gateways. Users with mail routed through these types of systems (ask your system administrator) may have problems participating in the list. 3.3. Interacting with the List Server

The LIMS Mailing list uses the ListProcessor [5 ] program (v6.0) by Anastasios Kotsikonas ('Tasos') as a list server. Some general guidelines for interacting with the ListProcessor using basic commands are given below. 3.3.1. Save the 'welcome' message If you choose to subscribe, please save the 'welcome' message (see Fig. 2) you receive from ListProcessor confirming your subscription for future reference, especially if you are not familiar with ListProcessor. It might look like a waste of disk space now, but in 6 months you will be glad you saved the information when you realize that you cannot remember what lists you are subscribed to, or what the command is to leave the list to avoid filling up your mailbox while you are on vacation.

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3.3.2. Sending ('posting') messages to all subscribers To send a message to all the people currently subscribed to the list, just send mail to lims @govonca2.gov.on.ca. This is called'sending mail to the list', because you send mail to a single address and ListProcessor sends copies to all the other subscribers. This address ( lims @govonca2.gov.on.ca) is also called the 'list address'. You must never send any administrative commands to that address, as it would be distributed to all the people who have subscribed (really annoying). Send them to the ListProcessor address ( listproc @govonca2.gov.on.ca) instead. 3.3.3. Sending user 'mailable' commands to ListProcessor The ListProcessor accepts a number of user 'mailable' commands to set options on your subscription or other administrative activities such as searching the list archives, reviewing the list of subscribers etc. A subset of the most important and useful ListProcessor commands excerpted from the ListProcessor on-line help and how to use them are explained below. Some general rules for issuing requests to ListProcessor o everything appearing in [ ] below is optional • everything appearing in < > is mandatory • all arguments are case insensitive e the vertical bar ( ' 1 ' ) is used as a logical oR operator between the arguments • requests may be abbreviated, but you must specify at least the first three characters ® < i i st > should be replaced with '1 ims' since you are probably only interested in the LIMS list. All commands must be sent to the 'ListProcessor address', [email protected] and not the 'list address', [email protected]. It is very important to understand the difference between the two. Sending messages intended for ListProcessor to the list address is like the phone company having one of those computers call all of their existing customers each time they install a new phone. You might forgive them the first time but you would probably give them an 'earful' if they did it again~ 3.3.3.1. The rNFOR_,~TrON command - getting more information on this list SYNTAX: information < list >

You can get a copy of the most recent LIMS Mailing List Admin Message by sending the command '~NFO~mT~ONr.IMS' in the body of your message. The LIMS list "charter' that describes the goals of the list and material suitable for discussion on the list is also included in the information page. This 'information' page is constantly under construction and your feedback on what should be included is welcome. Send suggestions to [email protected]. 3.3.3.2. The SET command subscription

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You can also tell ListProcessor how you want it to send your list mail and if you want confirmation of your messages being posted. Sending the SET command without supplying the optional arguments, returns a list of all current settings for your subscription. Otherwise, supplying one of the < options > with < arg [ s ] > changes the option to a new value for your subscription. Issue a 'help set' request for mo~e information. < opt: ions >

I. MAIL -set the mailing options for your subscription to one of four possible modes ( ' < arg [ s ] > ' below) @ -

NOACK -(Default) Send no acknowledgment message when user posts mail to the

list. ~cK -Send the user a confirmation of their message being posted to the list (recommended). posTPoNE -Do not send user any list mail u,til the MAIL mode is reset. - D~G~ST -Do not send individual messages but wait until messages reach 1000 lines or 24 hours have elapsed since last digest sent. The digests are numbered and have a table of contents and the full text of each message (Fig. 3). 2. Note: occasionally ListProcessor will set a user's mail mode to PosTPot~. for no apparent reason. If you suddenly stop receiving list mail, try issuing the 'SET LIMS MAIr. < [~CK, NOACK or DIC~.ST] > ' command before contacting the administrator ( millers @ gov.on.ca). -

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Sending the HELP command without arguments retums the help file listing all relevant commands (' [ t o p i c s ] ' ) . Otherwise, supplying [ t o p i c ] returns specific information on the selected topic. Topics may also refer to requests. To learn more about this system issue a ' h e l p l i s t p r o c ' request. To get a listing of all available topics, generate an error message by sending a bogus request like 'help me'.

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3.3.3.5. The RECIPIENTS command--seeing who else is listening

Fig. 3. Screen capture of first page of typical 'Digest' received from LIMS list server.

SYNTAX: < list >

3. CONCEAL-It is presently possible for other subscribers to determine that you are signed up to the list through the use of the 'R~VXEW' command, which returns the e-mail address and name of all the (unconcealed) subscribers. If you do not want your name to be visible, issue a 'SET LIMS CONCEAL' command. To reset to unconcealed, issue 'SET LIrIS CONCEAr.NO'

Get a listing of all non-concealed people subscribed to the specified list by issuing either the

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You may leave the list at any time by sending a 'SIGNOFF LIMS' o r 'UNSUBSCRIBE LIMS' command. 3.3.3.4. The H~.P command--getting more help SYNTAX: help [topic ]

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3.3.3.6. The STATISTICS command--seeing who talks the most SYNTAX: statistics < l i s t > { [subscriber Email address(as)] I [-all] }

Get a listing of non-concealed subscribers along with the number of messages each one of them has sent to the specified list. If the optional e-mail addresses are given, then statistics will be collected for these users only. For example: star lims userl@domain user2@domain

will generate statistics about these two subscribers. ' - a l l ' lists statistics for all users that have posted on the list (whether currently subscribed or not). 3.3.3.Z The ncDrx, SEARCHand Get commands - looking in the archives

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Get a list of files in the selected archive, or the master archive if no archive was specified. For the LIMS list, all list mail for a given month is archived to a file named ' l i m s . [ m o n t h ] ' and the ' a r c h i v e ' name is 'lims'. Ignore the 'path-to-archive' and '/password' arguments. SYNTAX: search < archive I path-toarchive> ] [/password] [-all] < p a t t e r n >

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Search all files of the specified archive (and all of its subarchives if-all is specified) for lines that match the pattern (Fig. 4). The pattern can be a UNIX egrep( 1)-style regular expression with support for the following additional operators: ' ~ ' (negation) '1' and '&' (logical OR and AND) ' < " > ' (group regular expressions) The pattern may be enclosed in single or double quotes. Note: '. ' (period) matches any character including a new line. This command will return a list of archive files that contain < p a t t e r n > . You must then issue a GET command to retrieve the appropriate archive file(s). Save the message specifying which archive files contained matches from the search command (Fig. 5) since the GET command returns the entire archive file (or part). You must find the relevant text ( < p a t t e r n > ) in the archive file using the 'search' or 'find' function in your e-mail client software. SYNTAX:

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I path-to-archive> [parts]

Get the requested file from the specified archive. Files are usually split in parts locally, and in such a case you will receive the file in multiple e-mail messages - an 'index' request tells you how many parts the file has been split into, and their sizes; if you need to obtain certain parts, specify them as optional arguments. If an archive is private, you have to provide its password as well.

4. The future With the popularity of the Internet still growing at an exponential rate, the LIMS Mailing List may

evolve to include a parallel Usenet newsgroup if demand is strong enough. Fortunately for those without newsfeed, ListProcessor and other mailing list software have the ability to link to newsgroups, echoing group posts to the list and list mail to the group. The W W W is by far the most popular medium for information access on the Internet these days and although the web does not lend itself well to group discussions, the LIMS Mailing List may also get a home page on the Web to act as a general information page and pointer to the list (and possibly the newsgroup) itself for those searching the Internet for information on LIMS. Several pointers to the list already exist and can be found by searching on the word LIMS with any of the more popular W W W search engines.

5. Finally The complexity of today's LIMS products and the requirements modern labs have with respect to their information management solutions are such that it Is very unlikely that any single lab or vendor will have an impartial 'expert' available to answer all your LIMS-related questions. However, the coll e c t b , knowledge and experience of the over 600 subscribers contributing to the list should be able to answer almost any of your LIMS queries.

References [ 1 ] M.D. Hinton, Laboratory Information Management Systems: Development and Implementation for a Quality Assurance Laboratory, Marcel Dekker, New York, NY, 1995. [2] S.M. Miller, Am. Lab., July (1995) 24-25. [3] H.D. Gillespie, LIMS/Letter, June (1995) 5&l 1 (e-maih limsletter@ aol.com). [4]Information on the 1995 International LIMS Conference is available from the LIMS Institute, 1416 Severn Street, Pittsburgh, PA 15217, USA. [51 ListProcessor (v6.0) informa6on is available by gopher (gopher://israel.nysernet.org.70/11 / computers/iistproc).

Stu Miller is Mineralogist and LIMS Coadministrator at the Geoscience Laboratories, Ontario GEOservices Centre, Ministry of Northern Development and Mines, 933 Ramsey Lake Road, Sudbury, Ontario P3E 6B5, Canada. Phone: 705670-5635; fax: 705-670-3047; e-maih .