Learn / User feedback
Q & A sessions
A conversation with Hoang Pham and Morten Jensen, of the modENCODE (model organism ENCyclopedia of DNA Elements) Project, which includes collaborating labs at University of North Carolina, University of Cambridge, University of California, Berkeley, San Diego, NimbleGen, the Dana Farber Cancer Institute, and the Weizmann Institute.
Q. Tell us a bit about modENCODE and the research you are doing.
modENCODE is a network of scientific groups funded by the National Human Genome Research Institute (NHGRI) to identify all of the sequence-based functional elements in the Caenorhabditis elegans and Drosophila melanogaster genomes. The scientific group we are part of consists of 7 individual labs. It is our focus to identify and technically validate functional elements that control chromatin and chromosome behaviour in C. elegans. To this end we employ chromatin-immunoprecipitation in combination with microarrays or high-throughput sequencing and aim to produce data for around 125 proteins and histone modifications. Datasets that pass our validation criteria are made available to the public for benefit of the scientific community in general. Because high integrity and quality of the data are top priorities, keeping track of it is pivotal to the success of the project.
Q.You were using a wiki originally for your data, before adopting eCAT. What was it that attracted you to eCAT and how have you found it better than the wiki?
That’s right. We initially stored our data on a wiki using embedded spreadsheets. We soon learned that this was not a feasible option due to the complex structure of the data, and we started shopping around for alternatives. When we were tasked with searching for an alternative to the wiki, or free web-based alternatives, we found that they were lacking in features and/or support. Initially, we were looking into LIMS, but those platforms were highly specialized, very complex, and expensive. eCAT is a better fit for us because of the fairly intuitive UI, the ability for the database structure to be modified by the end user, cost, and importantly, customer service. We have been highly impressed with the level of customer service offered from Axiope. It is clear that they take pride in their product, are concerned about the customer’s experience and are always receptive to suggestions for feature additions and/or changes.
Q. Tell us how you have been using eCAT.
We record both simple data, such as protocols and info on reagents, as well as more complex data like experimental datasets that links records from different parts of the database. Due to the thoughtful UI of eCAT, it took little effort to get all wet lab members trained to use eCAT to facilitate data entry. Members of our labs have also been starting to use the e-notebook feature of eCAT. They find it very easy to enter their experiments and organize their data. They are starting to realize the power of allowing them to more natively integrate electronic sources of data (documents, images, web links, etc.), which was something not readily accomplished with a paper notebook.
Q. I know you are using eCAT for inventory management as well as to manage your general data. How is that working out?
We record what is stored in each lab, but not where it is stored within each lab. We realized that we didn’t need a robust solution for tracking inventory levels and locations to great detail. However, this type of feature is useful and provides a graphical format illustrating organization of freezers, shelves, racks, and box contents.
Q. How are you making use of Desktop stores to manage files in eCAT?
Desktop stores are easy to use once setup, and the similarity to standard Windows folder structure makes it user friendly. Desktop stores have streamlined the process of uploading data to eCAT. Having a "local" folder on the desktop to allow dragging and dropping of files, as well as deletion, is better than the previous alternative. So it has worked out pretty well for us. We store different types of data there, each lab having a standard Desktop store structure.
Q. How did you introduce eCAT to members of the consortium?
At the time we were introduced to eCAT we had already changed databases a couple of times and were getting tired of all the work associated with migrating data. We were therefore looking for a 'final' solution, and only committed to eCAT after feedback from users of the group. For this, we set up a minimal database and had test users carry out a range of different common tasks having only a brief Powerpoint presentation as an operations guide. This worked out well with a unanimous vote to adopt eCAT. We then refined the operations guide and introduced users with a live demonstration at our annual meeting.
Q. modENCODE is a distributed group of labs from around the US and several other countries. How is eCAT working out as a single environment that enables people from multiple locations to enter and share data?
It is working out very well. eCAT has enabled us to store and share data easily and safely.