Dear EvolDir community! I asked for sample management software a few days ago. Here is the original post: ----- we are searching a way to get rid of Excel tables of our samples in Dropbox or network drives. Would you be so kind and suggest solutions regarding the management of samples? Our samples are regular molecular ecology stuff. Sometimes we have multiple samples from the same individuum, and also multiple samples types. Otherwise we do not need anything special. It would be nice if the sample management could be online etc. To be honest: We do not exactly know what we need We rather wish to explore some options. If you can suggest a software/system, would you as well very briefly let me know which are the pro and cons in your daily use, and for what applications you have it? I'll of course repost all collected info here on EvolDir in a few days. ----- And these are the answers that reached me. I will return all answers to you without actually sorting out the ones that I think would not work so well. That is because your idea of such a software may be different from mine. Hope this is useful! Cheers, Robert (robert.kraus@uni-konstanz.de) 1. We increasingly rely upon Google Spreadsheets. It's all saved in the cloud as part of Google Drive, is free, and it is of course very easy to share with multiple people such that certain lists of people can view the data and others can edit it. I suggest backing up regularly to a private spreadsheet, though, because if someone with edit access erases it, it's gone (same as for documents shared on networks.) 2. we purchased a FileMaker server license and five client licenses installed on lab computers. We then created our own Filemaker database. It works great. The server software takes care of the backups and allows multiple users to modify the database while enforcing integrity of the data. You can publish the database on the web and restrict access. There is a bit of a learning curve though. 3. we have been looking into options to use a MySQL database for sample management. It has the flexibility that you can add any type of metadata you want provided you organise the database carefully from the begin on. However, I'm interested in any feedback you get from your query and would appreciate it if you could forward it to me. 4. we have established in our molecular lab a SQL database managed by the system OpenBIS from the ETH (http://www.cisd.ethz.ch/software/openBIS). Possibly it is a very big hammer on your data but it is very flexible and extensible over time. The simplest setting would be: Store your samples in the database and add observations as attachments (excel tables, etc.) to it. The next step would be to create database entries for the different experiments and you could link the samples to this (and could also backtrack from experiments to the samples afterwards, which is quite nice for supervisors or if you try to remember what you have done month ago). The management/installation is not very easy but with a little knowledge about databases, SQL and linux doable in at least 2 weeks. A complete and sophisticated setup might need 4 weeks or even some month while learning the system better and better to get the whole workflow optimized. 5. Perhaps our VoSeq database would be of use to you? https://github.com/carlosp420/VoSeq and http://nymphalidae.utu.fi/cpena/VoSeq_docu.html 6. I would very much recommend JMP (www.jmp.com) as the data management and analysis platform. It's a popular statistical package and it's great as such (not cheap, though), but it is particularly good at data management. It allows to easily summarize data by any combination of columns, merge files by matching values two or more columns (with or without retaining non-matches or dropping multiples in either table), split and stack columns by specified values, etc. More expensive ProJMP version includes the same functions in the form of database management tool. Even more expensive JMP Genomics version includes all kinds of sequence, genotype an expression data analysis tools, but this maybe more than what you are looking for and it is expensive. 7. We do the things you mention with our software www.earthcape.com Please let me know if you want to have more details about it. Perhaps a skype call. It would be interesting to learn details of your needs and tell you about what we can offer. 8. We use Lab Collector, it has all the capabilities that you probably need and is user friendly and web based. Can be a little clunky for entering large quantities of data, but it is great when you have a whole team needing access to shared information. We use it most for colony management and sample inventory, but it has the capability to include sequence data etc. It was also one of the more cost effective solutions that we found. http://www.labcollector.com/ 9. I use the biocode plugin for Geneious. http://software.mooreabiocode.org/index.php?title=Main_Page Pros: you can add several metadata fields to each sample, you can have several DNA extractions from the same sample (which you could use as a proxy from different tissues, maybe?) and keep a track from your samples from extraction to sequence. I haven't used it in a "collaborative mood", but I know is possible and can be done online. Cons: tutorials are not super clear (or they weren't) and takes some playing around to fully get it and, very important, although the plug in is free you need Geneious Pro to use it, ie you would have to pay for this (student discounts available and license can be use forever with a limited number of upgrades). Hope this is of any use, looking forward to hear back what others are doing. 10. If you're looking to get off dropbox, then you can set up an identical system with no subscription or data limit with Transporter. I set my own personal one in my house and I sync it to my university computer and my home computer. I set mine up with a 1TB hardrive, but you can add whatever hardrive you have, and I think some models of transporter let you use multiple harddrives. It works identically to dropbox, only instead of being on the dropbox website, it's on a tiny server (palm sized) where you are, which is safer. Also, you can have it synced, so that everything is on all your computers AND the transporter, or you can have a folder that is ONLY on the transporter, and so doesn't take up space, but can be accessed whenever you want. You can also share individual folders, assign space to different people etc. I highly recommend. This is their homepage: http://www.filetransporter.com/ I use the transporter sync for my personal/work stuff it works with a harddrive you provide of up to 4TB (Can't see why not higher but it says 4TB on site): http://www.filetransporter.com/for-individuals/ They have larger things for companies/businesses so maybe you could look at that. You can often find them cheaper in other stores, but this site has all the info. 11. Have you looked at the Field Information Management System that the Moorea Biocode has developed? It works with Geneious. I find it a little much, but it is very comprehensive. http://www.mooreabiocode.org/pages/lims *Dr. Robert H.S. Kraus /Assistant Professor/* - Disease Ecology and Evolutionary Genetics http://www.orn.mpg.de/642473/Disease-Ecology-and-Evolutionary-Genetics I am on Twitter @rhskraus! /Group Wikelski; Biology Konstanz University, Room Z805 D-78464 Konstanz / /Max Planck Institute for Ornithology Am Obstberg 1 D-78315 Radolfzell / tel. 0049-(0)-7531-88-3479 robert.kraus@uni-konstanz.de /_"Chance favours a prepared mind"_/ Robert Kraus