open source Laboratory information management system - health-monitoring

We are looking for open-source solutions for Laboratory. we are not sure enough with is the good choice for us. any body with LIMS experieces please help.
Thanks you very much

I can tell you you are not giving anywhere near enough information to get an answer. Could an open source LIMS work? Yes. But there is many many LIMS out there and depending on your needs it may or may not work for you contact a company like LabAnswer to get a reccomendation.

To save you time, I would advice to start by reading some recent published papers about open source LIMS. And here is one:
http://scripts.iucr.org/cgi-bin/paper?S0907444905001290

i have just put a depot of my project at https://github.com/matoeilD.
It is a LIMS type project management system, made up for a biomedecine laboratory and it is developped with Ruby on Rails.

Related

Search for VMS documentation tool (VAX document ?)

Many years ago I worked at a DEC-shop. We used a tool called Document (as far as I remember) to create documentation. It was provided by DEC and created the same layout as the original DEC documentation. Which is as far as I'm concerned a milestone in layout and typesetting.
Researching the web I found a more or less obscure company which sells this tool for Open VMS. But I would prefer an open source replacement.
Any help ?
Greetings Till
Touch Technology was, and perhaps still is, an interesting company with interesting folks like 'Mr Dan'.
They picked up a good bit of Digital software in a fire-sale and had some good stuff such themselves such as performance tuning tools and a 4GL (Intouch... available on OpenVMS Freeware).
The company appears to have moved one, judging by their current website front door which does not dwell on the old stuff , but you could do worse than try contact them.
The back door still list DECdocument: http://www.ttinet.com/documentation.html
Good luck!
Hein
If you're still looking for a solution, have you thought about LaTeX? The markup syntax isn't radically different from VAX DOCUMENT's SDML. They both have the same back-end; the final steps in processing an SDML file involved running it through TeX.
I would think the best solution would be DocBook, since it is also an SGML-ish format. You might be able to translate a substantial portion using XSS.

Is it possible to get un-minified source for redquerybuilder?

Is it possible to get un-minified source for redquerybuilder?
I like what I see but need to change quite a lot for my application.
thanks
Ben
I'm afraid it is free but closed source software at the moment. We are trying to understand what level of interest there is before thinking about licences and tidying up the code.
Any particular features you need? Either way we definitely want to allow people to customise without changing the core code.
Update 19/8/2013 - Now open source under the EPL licence https://github.com/salk31/RedQueryBuilder

Bug tracking for legacy physics models

I am the lone software engineer on a team that develops physics models (approx 30,000 lines of code). The rest of the team consists of scientists who have been developing their codebases for about 20 years. My workflow goes something like this:
Scientist requests a new feature
I implement it
Via testing & validation, I find a serious problem somewhere deep within the numerics
Scientist requests a new feature (without fixing the problems identified in #3)
Our problem seems to be that bug tracking is done via e-mail and post-it notes. Busy work schedules let bugs slip under the radar for months and months. I think some formalized bug tracker (i.e. Trac, Redmine, Jira, FogBugz, etc.) could help us. The following features are essential:
Incredibly easy to use
Integrate with version control software (we use Subversion)
There are plenty of posts that suggest which bugtracker is "best"... but I suppose that I am more interested in:
What's your experience in whether or not the overhead of a bugtracker is worth it
How do you convince a physicist (who follows poor software engineering "best practices" from the 70's) that a bug tracker is worth the extra effor?
I get the feeling that if I install a bug tracker, I'll be the sole user. Has anyone else experienced this? Is it still useful? It seems like the team would need a certain amount of "buy-in" to make a bug tracker worth the additional overhead.
Bug trackers are definitely worth it, in part because they formalize the work-flow required to implement new features and fix bugs. You always have a central place for your work load ("My bugs", "My tasks", etc). Pretty much every environment that I've worked at in the last few years has had a bugtracker of some sort so I'm not sure what to recommend in terms of buy in. Do you have more than one scientist coming to you for feature requests/bug fixes? If so, then perhaps you could use the bug tracker as a conflict resolution system of sorts. Do you have a boss/manager? Then having a bug tracking system would provide a lot of insight for your boss.
In general, as a software developer, bug trackers have been very useful. My suggestion would be to think of ways that a bugtracker would enhance your & your coworker's life. Maybe do a quick demo.
HTH.
In my experience, the overhead of a bugtracker is noticeable but definitely worth it! The catch is that if you decide to use a bug tracker, it can only succeed if everyone uses it. Being the sole user of such a system is not quite as useful.
Having said that, even if I am the sole user (which tends to happen a lot), I still install the bugtracker (typically trac). If you use it religiously (enter every thing that comes in through different means as a bug and ALWAYS refer to bug# in your replies), the team generally tends to pick it up over time.
Enter milestones (or whatever your tracker of choice calls them) and link bugs to them. Whenever someone asks what the progress of something is, call up the milestone report or equivalent and SHOW THEM. This helps convert people from thinking of the bug tracker as a nuisance to realizing that it can be a source of invaluable information.
I suggest taking a look at Strategy 2 in this Joel On Software article. He basically argues that if your company doesn't use bug tracking software, you should just start using it for yourself, and demonstrate how it helps get things done. Also ask other people to use it to submit bugs so they see how easy it is to use.
Even if you're the sole user (it happened to me once), it's worth it. You can start saying things like, "Bug 1002 is blocking. Who can help me with that so we can move on to this and that feature."
We found redmine to be a better than trac simply because it is easier to use. It does lack some of the features found in some of the other systems, but this also means there is less stuff for non-programmers to have a problem with. It's also very nice because it allows someone other than the programmers to get a feel for the current state of the system. If there is a large number of critical unclosed bugs it is easier to make people understand that their requested feature will have to wait a little.
This is a similar question.
What's the Most Effective Workflow Between People Who Develop Algorithsm and Developers?
It does NOT speak to which bugtracker is best, but it does speak to how to convince the physicists to buy-in.
Using subversion? Here's a /. post that is helpful:
Best Integrated Issue-Tracker For Subversion?
An in general, here's a Comparison of Issue Tracking Systems.

Is it better to do roll-your-own or ready-built forum software?

As part of a wide ranging job for a cystic fibrosis support organization, they'd also like a web site set up and I've decided on Apache running on Linux (due to its security and low cost mostly). Other than (fairly) static content, they also want a forum where people can discuss issues with the condition - it'll be attached to a hospital chain so there'll be plenty of medical staff there who know little about the web.
I can handle all the specific coding and Apache setup since I've done it before but I'm interested in people's opinions as to whether I should roll my own forum software or get a hold of some ready-built stuff. I've not had any experience with forum software but I could generate my own (initially buggy, I'm sure) in a month or so.
It'll require registration and login to leave comments (but guest access just to read) and I'd like it to be 'pretty' (excuse me while I remember damning customers for providing similarly vague requirements specs :-) but not necessarily infinitely-configurable with skins/themes/etc.
If anyone has some compelling reasons (and experience with specific products that can provide what I need), I'd be interested in hearing about them. Alternatively, does anyone have any 'gotchas' they experienced while coding their own forum software?
Advantages to rolling your own:
a non-standard custom-built system means you'll be less prone to "standard" attacks (e.g.: a vulnerability in PunBB) since bad guys tend to bother with exploit-hunting only on widely-deployed systems (more return on their investment)
absolute control over how your system works and looks
you'll learn a lot
Disadvantages:
you'll repeat mistakes other people have already solved
it'll take you longer to get up and running
long-term it'll be more maintenance (since you have to fix bugs & add features yourself).
you can't "leverage the community" -- if you choose an off-the-shelf forum that has a plugin system then there's a whole bunch of community add-ons that won't be available for your custom forum software.
There's a GIANT list of forum software on wikipedia -- there's most likely something in there that will suit your needs that you can get up and running quickly.
IMHO the old "don't build what you can buy" adage applies to this (well, the web 2.0 version is obviously "don't build what you can download"). Have a look around at the available forum software, pick one that covers 99% of your needs and tweak it to do the rest.
If you still want to build your own forum software that'll probably be a cool side project but if the job is to get a forum up and running, then go and download one - don't try to mix up the desire to do cool stuff and the day job unless the day job is just to do cool stuff only.
One of the best-kept secrets on the internets is a little gem called FUDforum, by Ilia Alshanetsky.
And yes, it's the same Ilia who wrote xDebug's original profiler code, improved the caching in MMcache, fixed several security bugs in libmcrypt, and who was the release manager for the PHP language from 4.3.3 to 4.3.6+. He is, as my friends in Boston would say, wicked smaart.
Because of this, FUDforum is robust, ridiculously fast and more secure than probably any other part of your web application will ever be. It comes with a neat install script and it has all the features you'll need.
Plus, it's not a high-profile target like phpBB or vBulletin, which means you won't have to worry about spambots constantly banging on the gates.
Having written my own forum software before...
It seems like a simple problem, but when you get into it, you find that there's a lot of little things that you'd like to do nicer, and it takes a lot of time. Mine was cool and all, and I did get paid for it, but if I was doing it over again (which has also happened), I'd use a customizable pre-made solution, and spend all my spare time doing something productive. :)
Forum softwares tend to have rather complex minimum requirements. A few things you are very likely to need do matter what you do:
Forum/thread/post hierarchy;
User system;
Security system (eg user/admin classes and all kinds of restrictions for users);
Gathering statistics;
BBCodes or some other minimized markup language (NEVER allow users to do full HTML);
File uploads and avatars;
Bans and other punishments;
CAPTCHAs;
etc.
Ready made forum systems provide this out-of-the-box and lots more. Setup is mostly easy too. Why do it all over again yourself?
My answer would be: don't reinvent the wheel, there are plenty of fora software out there. My preference would go for RForum if you need only that.
I'd say, don't waste your time. phpBB 3 is pretty stable, usable and feature-rich forum. We use it at work (for our internal discussions), and I really don't have anything bad to say about it.
I'd concur with most of the above posters that since you want something which appears fairly standard, why reinvent something that already exists?
Like any development, creating forum software is probably much harder than it looks! There will be problems solved in the existing software which you haven't even considered.
It's worth adding that if you do require any specific additional functionality, you can always build that on top of an existing solution anyway, which is especially easy if you have the source code (whether open source or commercial).
From the sounds of the website that you are building, there is the potential for the forum to be a highly useful and visible resource, it would be good to go with something that already exists, due to the quality of a lot of the products out there and the rich communities that surround them.
I think that vBulletin, although a paid for product, would suit your needs and give you a great base to build a community on.
vanilla is pretty bare bones and easy to configure, perhaps find a system which is easy to extend vs building everything yourself
Ready built until you have some really unique features needed that can be tied to money it will make you.

One man bugtracker?

Recently I've been doing lots of weekend coding, and have began to really need a bugtracker as things are gaining speed. This is probably the worst case scenario because I basically have to let things cool down over the week,so I simply can't remember the bugs in my head. So far I've been using a text file to jot down bugs,but I'd rather use something a bit better.
The biggest points here are ease of use and very little setup time.Don't want to spend more than an hour learning the basics and trying to install something. Also in my case I'm on a Mac so that would help, but solutions for other platforms are welcomed as they will likely help others.
FogBugz has a student/startup edition that's free indefinitely, for 2 or less users.
Personally, I use Excel. (Wait, come back, I'm not crazy!) For a bigger / team project, I've gotten a ton of mileage out of Bugzilla, but that tends to be kind of overkill for a one-person project.
But, a well-organized spreadsheet, with columns for things like "status", "description", "code module", "resolved date," etc, gets you pretty close to what you'd need for a small project. Sorting a spreadsheet by column isn't anywhere near a search, but its a whole lot better than "find in text file."
Heck, if you use Google docs rather than excel, you can even publish the thing as an RSS feed and get it anywhere.
And, the major advantage is that the setup time and learning curve are both effectively nil.
Addendum: And of course, the instant your "One-Person Bug Tracker" becomes a "Two-Person Bug Tracker" you must switch to something better. Bugzilla, FogBugz, anything. Trust me, I've been there.
Trac or Redmine are both pretty good. I don't know how easy they are to set up on a Mac.
It's worth mentioning that FogBugz also has a free version for up to 2 users, which would suit you. It is hosted so there is no installation and you can use something like Fluid to access it in its own window.
I don't think you need a full blown bugtracker for your scenario.
Try tiddly wiki, store each bug in a tiddler and give them tags like 'open' or 'closed'.
There is no installation required (only one html file), and it's very easy to use.
And platform neutral.
If you're working on a LAMPP stack, then for ease of setup and use I would probably recommend Mantis. It's written in PHP / MySQL and the only installation involved was specifying where the database should be created and what credentials should be used.
Oh, and its FOSS.
I would suggest Omnigroup's Omnifocus - it's an excellent task tracker, and if you just make the mental leap from bug to task, I think it works famously for one man projects as well as being an excellent way to organize your no doubt burgeoning task queue.
Eclipse has a really interesting system--I don't know why so few people seem to know about it.
It's tied in with their to-do list. It gives you the ability to enter bugs with as much or as little info as you like. You can tie it to versioning or an external bug tracker if you like. It's a decent bug tracker in itself.
The real trick is how it works with your source code.
Before you begin work you select a bug from the list. All the time you're coding, it tracks what files you are editing. It can close old tabs for you, and will also highlight areas of the source tree that you have modified a lot.
The nice thing is, you can go back to any bug you've edited an you will get your "Environment" back. Not only all your notes and stuff, but the same tabs will open up and the same sections of code in the navigator will be highlighted.
Also eclipse works with virtually any language, it's not just restricted to Java...
let me put in a good word for ditz - it's a bit bare-bones, but it has the invaluable feature that bugs are checked into your repository. it's also very easy to use once you get used to its way of doing things
You can use fogbugz for free if you're a one man team.
It's super easy to use and quick to learn.
They made it so that bugs are really easy to enter, no mandatory fields.
I'm the author of BugTracker.NET mentioned in another post. If I were looking for a tracker for JUST ONE PERSON with MINIMUM hassle, I'd use FogBugz, because it's hosted. No installation, no need to worry about backups.
But, what are you doing about version control? Don't you have to worry about that too, and backing that up? If so, consider something like Unfuddle or CVSDude where you can get BOTH Subversion and Trac, or Subversion and Fogbugz.
I use Mantis at home and I'm happy with it. It can be a pain in the arse to get it working so you can choose to download a free and ready-made VM installation. Cannot be easier than that,
Maybe a spreadsheet would be the next logical step? I know it sounds really un-sexy, but if you're the only user, you don't have to worry much about others mucking it up, and it adds a few basic features over a text file like sorting. Then if you later need to graduate to something RDBMS-backed, you would likely have a feasible import path. I just know that for me, when working by myself, I don't tend to get around to putting bugs in anything that requires more care and feeding than that (of course when working with others the collaborative needs make a more defined repository a requirement, but that's a different story).
EDIT: After noting the availability of free, hosted access to FogBugz, I'm re-thinking the bar for care and feeding...
RT from BestPractical is great.
I also get a lot of mileage out of just keeping a list of items in a text file with vi, if I can express them all in one line. This is usually for many small todo items on a single component or task.
I've tried bugtracker.net and even though it's a little bit rough on the edges, it's free and was built with ASP.NET:
http://sourceforge.net/project/showfiles.php?group_id=66812
Are you using a source control repository as well? If not, you really should, even though you're only a one-man team.
My personal preference is to use a VMWare Virutal Application (free) that offers no-hassle setup gives you access to both Trac and Subversion. You can find many different virual appliances through searching. Here is one example of getting a Trac/SVN virtual appliance up and running:
http://www.rungeek.com/blog/archives/how-to-setup-svn-and-trac-with-a-virtual-appliance/
Trac is an excellent project management tool that sports a bug tracker, wiki, and integrated source control management. It's adaptable to your needs, and fits me very well personally.
I use bugzilla for this purpose. Plus for me was that it has integration with Eclipse (precisely with Mylyn). FogBuzz has it to but AFAIK it is nonfree.
Plus it sits on my laptop so I can code and add/remove bugs when offline (it was biggest disadvantage of hosted solutions for me)
Installation was not a problem in Ubuntu (and any debian-based distro I suppose).
I dig ELOG in those cases, it's more of a personal blog, but it's easy to handle and install, the data is local on your computer and you can search all entries via fulltext. Always sufficed for me.
If you have a Windows box with IIS and MSSQL (including SQL Server Express), you should look at Bugtracker.net. It is free and open source (you get the source code), and it is extensible.
Even if you are a one man shop, having a free bug tracking system with this much power will allow you to grow over time, because it is fairly easy to add future users into the system.
You can also customize it for the look of your organization, business or product.
Ontime 2008 by Axosoft is free for a single user licence. It's industrial strength and will give you alot more that just bug tracking!
http://www.axosoft.com
Jira which now has free personal licenses.
I am using leo for this purpose. To be more specific, its cleo plugin.
Of course you might need to spend some time to get used to leo, but it will pay off.
A flat text file is just a list, an Excel spreadsheet is a two-dimensional list.
leo lets you keep the data in a tree! And it also has clones.

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