I'm looking to create a database of cell lines I use and their characterisitcs i.e pathways active. I also want to add experimental findings i.e effects of drugs on the cell lines. Excel won't do. Ideally it needs to be a database that can be searched and added to easily. Does anyone know of any software that could be useful so that I can easily look for a cell line and see all the information I have gathered on it?
We set up a Filemaker Pro database system to track information in the lab. One database for cell lines, one for plasmids, one for primers and one for reagents. Filemaker pro lets you view in various formats and is highly customizable and pretty, but if you want simple, just use an Excel spreadsheet. The HHMI web site for early career investigators has some good resources and advice: http://www.hhmi.org/resources/labmanagement Take a look at chapter for record keeping advice http://www.hhmi.org/resources/labmanagement/downloads/moves2_ch8.pdf
I agree wholeheartedly with Piers. We use Filemaker Pro as a relational database management system. The beauty of this system is that it could be readily integrated with online cell resource data from ATCC as well as any information generated in-house about a particular cell line.
You can use also Endnote. On it, you can create custom field and it works pretty nice. Good luck!!
The best tool for lab managment is https://www.quartzy.com or if you want to run it on you server you can have Labstore http://www.bioinformatics.org/phplabware/labwiki/index.php
at one point I worked with a group who were creating a database of different cell lines tracked by timelapse microscopy for outcomes such as mitosis, apoptosis etc at the single cell level. I found a publication related to it (http://www.ncbi.nlm.nih.gov/pubmed/17387278) but can't find the data base itself. The PI is Dr Rachel Errington ()University of Cardiff) and is very approachable so she may be able to help you?
I would suggest FileMaker Pro (FMP). I have used it for years (since early 90s) and it does the job. For - it works, it does the job, it is a databases (i.e. it is not excel); Against - need some understanding of database normalisations and ERDs, expensive. I have used FMP for everything from keeping an address book, through to keeping publication/reference lists, and to using it to keep my lab book.
If you are a complete database novice then I would suggest you look at Bento (also made by FMP people - a bonus is if you start on Bento you can move the data to FMP later). Bento is like excel but has much better searching capabilities.
A wiki is a nice idea (but again you will need some experience of php and MySQL to set that up). Or you could just go MySQL.
We are also using the Filemaker Pro database system in the lab. It works well for us.
We use LabCollector, which while expensive, is a very good lab data base for all your reagents as well as cell lines etc
I set up a Sharepoint site for our lab to store and shera critical informations such as cell lines, plasmids, lab supplies, and all their related files. It works very well for us, and has the advantage that multiple lab members can open, and even edit, the same file at any given time.
Do you need chemical structure search capabilities to search for the drugs, similar compounds, structurally related compounds, etc.? Then you need some chemistry-aware database system.
You could try using XAMPP http://www.apachefriends.org/en/xampp.html which would be easy to use and you can as well import your excel sheets into MySQL within xampp and get going..or you could try microsoft access..
I would consider PostgreSQL as it gives you all features you need plus you can add Chemical search capabilities. All for free.
Follow the link below..
Pancreatic Beta Cell Lines and their Applications in *...* - Altweb
altweb.jhsph.edu/*altex*/.../*altex*_2_10_ske...by M Skelin - Cited by 22
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with the help of language programming, you can create a database. For GUI (Graphical user interface), java, C++, or perl could be used. for database creation you have to learn about RDBMS like SQL, Oracle or xml as well. R-programming could also be used along with the r-sql and r-java. After finishing, this work could be uploaded as online database of cell lines along with their characteristics.
We have build several fairly complicated database systems for culture collections and other applications in Filemaker Pro. It has a very user friendly interface and there is no need for knowing code to use it. Many other systems will do, but an important message before you start any database: ask yourself what information you want to get out of it in the future, not so much what you want to put in. You can always add info, its getting the info out that has to be in the database structure from the beginning.
You could use boxit, it is not only for cell lines but also antibodies, plasmids, etc. Not extremely user friendly, but it does the job if you get used to it.
This is great idea, but getting reproducible results with cell lines even within the same lab is a challenge. A database would have to v. carefully specify cell plating and doubling time. Detailed methods for adding drugs to cells are needed. If a database could document IC50s for different drugs and explain which experimental factors lead to changes or errors in IC50s...it would be great !
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