Tutorials

There are several ways of using the service.
On this page, we will explain four typical use cases. Each case will be a guided tour for a service on BioAtlas, along with relevant links for the particular case.

1) Using the World Map » Go to world map

If you don't have data on your own or just want to browse our existing data, use the world map.

The World Map features known places for where Archaea/Bacteria has been found. The sightings are based on 16S rRNA data exported from those GOLD Database sequence projects that contains geographical location data, and has classified using Mothur.

On the page:

On the left you will see the tree corresponding to the phylogenetic tree for both the Bacteria and Archaea kingdoms extracted from the GOLD data. The tree uses the SILVA taxonomy as reference. Use this tree to select/deselect species to enable/disable markers from the map.

If you can't find the species you were looking for, first try to use the search box located above the tree. If this still doesn't work, this could be explained by one of three cases:
  1. The name of the organism that you are looking/searching for, are not the same as the one dictated by SILVA.
  2. The organism isn't within any of the 16S rRNA strains extracted from the GOLD data. (most likely)
  3. The organism might have been in one of the strains, but our classification using Mothur didn't find it.
On the right you will see an instance of Google Maps, with markers on top of to it. Each marker corresponds to a GOLD sequence project. Clicking on a marker will open a window containing links to and information about the project, and will also contain the organisms filtered by the current selection in tree to the left.
The map also features a heat map button, here each point has a strength with a linear proportion equal to number of bacteria hits from the tree on the left.

2) Using the User Maps » Go to user maps

You can also use the user maps for browsing.

The User maps are user created content with locations that maps corresponding data sets, see tutorial 4.

On the page:

This page offers you a list of maps allowed for you to view. Select one by either clicking on it's picture or on the name of the map. On the map page you will see a list of accepted user maps, some might be build by us, some from other users.
Clicking on any of them will direct you to a page very much structured like the World map page. The page features a tree, and use markers to see what resides on what body part/location represented by the map. You can use the tree to left to filter what you see on the right. In addition to the actual map, you will also see a link in the top of the screen referencing to the article the source data is constructed from, along with a colored bar indicating the relative abundance for the map based on the current selection.

3) Filtering the markers using your own data » Go to job page

If you would like to add a batch of 16S rRNA strains on your own, use the classifier.

The classifier allows you to upload one or more FASTA files, and then let Mothur classify those on our server. You will not only get the classifications given by Mothur, but also a mapping to both the World map and User maps to where the Archaea/Bacteria has also been found based on the data you provided. If you just want to test the system, the page also offers a way to try out this part by selecting a test data set.

On the page:

The classifier features a web form. From here your will be able to, in order of appearance:
  1. Selecting a file mode, the file mode let you select between using your own data or the provided data sets.
  2. Defining a name for your job, you can leave this blank. This is solely for your own organizing purpose, if you want to return to the job later.
  3. Setting parameters for the classifier:
    1. Kmer size: The sequence will be split into chunks (K-mers), define the size of the chunks you want to use when comparing.
    2. Cutoff: During classification, an estimate for how 'good' the sequence is compared to what is classified as. The cutoff defines at what threshold the classification should be discarded, think of it as discarding all below a certain confidence score.
    3. Iterations: When classifying a sequence, 1/8'th of the k-mers will be removed and the rest is checked against the database. This is repeated during each iteration. This is used to find the confidence threshold.
When you are done defining your desired settings, click "Add files" if you want to add your own files. In the end press "Submit job" and your job will now be running on the server. When the job is done, you can access it through your Dashboard, here you will be presented with the results from your job.
Also, you will receive a filtered world map, based on the results of your uploaded data. Furthermore, you will see the user maps filtered based on your data, click on any of those to go to a filtered version, if no user maps are present, your data will not intersect that of the maps.

4) Adding a user map » Go to user map builder

If you would like to contribute or have a user map on your own to compare against, use the user map editor.

The user map editor consists of two phases, one for uploading your database file, the other for marking positions of the microbial locations. If you have sequences from microbial samples (residing on hosts, surfaces etc.) you can upload matrix file and one or several pictures to our server. (note: this requires an account, you can create one freely at the top of this page).

1 Upload phase:

The procedure follows the same routine as that of Case 3. First please specify name, source article name and link to the source article from where you got the data from. This information is used if we want to make the map public for everyone to use. And at last specify what kind of database file you provide. The databases are SILVA ID's (which refers to the unique id's of the SILVA Ref NR 128 data set), SILVA taxonomy, NCBI taxonomy, or the GreenGenes taxonomy. The database file is structured as follows:
  1. First column specifies the IDs/taxonomies.
  2. First row specifies the environment (bodyparts, surface etc).
  3. Examples of each data set is listed on the buttom left of the page.
In the end, upload your desired data set and construction can be done.

2 Build phase:

Next, you will be presented with the editor. To the right you will see the locations extracted from your database. Click any and place them on the maps accordingly to your knowledge of where the maps resides. When you are done click the Finish button and your map should be generated and ready be ready to use for either browsing or comparing with jobs.