4 Octover 2018
The biomine and human databases have been updated! After more than 2 years of fixing bugs and updating the networks, there are two new databases: biomine_3_oct_2018 and human_3_oct_2018.
There is another very important update: the server which hosts Biomine Explorer now supports HTTPS.
2 August 2018
Three new plants have been added: Chlamydomonas reinhardtii (green algae), Populus trichocarpa (black cottonwood) and
Vitis vinifera (wine grape).
The updated plants database is called plants_2_aug_2018.
The old plant database plants_1_jul_2016 was retired and is no longer available.
26 January 2018
Two new plants have been added: pearl millet (Pennisetum glaucum) and bread wheat (Triticum aestivum).
The updated plants database is called plants_26_jan_2018.
18 January 2018
A new data source called CNN has been added for Arabidopsis thaliana! CNN is an abbreviation for "comprehensive knowledge network" which is
a hand-crafted network, compiled from different sources. It was prepared by dr. Živa Ramšak from the National Institute of Biology, Ljubljana, Slovenia.
The updated plants database is called plants_18_jan_2018.
13 December 2016
A small bug was fixed which caused that in some special cases the search result was not returned (the server returned 404 error instead of the graph).
21 July 2016
The search interface has changed! It now supports three types of search:
- neighbourhood search (same as before)
- connection search on 2 query sets
- connection seach on 1 query set (between all nodes in the set)
All three types were already supported by Biomine but were not enabled by Biomine Explorer. Its interface now provides two query lists (source and target) where query terms can be added or imported. Please see help on search functionality on the main search page
1 July 2016
All databases were updated. The latest databases are: biomine_1_jul_2016,
human_1_jul_2016 and plants_1_jul_2016.
Due to changes in OMIM licence some OMIM data (textual descriptions) is not available anymore. Updates of OMIM in Biomine are expected to become less frequent because each academic OMIM download is granted only upon a formal request.
9 February 2016
Graph visualisation has been updated to show a thick green border around query nodes.
They are now easily distinguishable from the rest of the graph.
There were also few fixes as well such as proper formatting of query terms in the search interface.
14 January 2016
All databases were updated! The latest databases are: biomine_13_jan_2016,
human_13_jan_2016 and plants_13_jan_2016.
Also, few additional fixes were implemented in the user interface.
8 January 2016
It's been exactly one year since the new Biomine went online.
There is a huge number of updates in the web interface! Biomine Explorer now supports user management and private graph repositories for each user.
Anonymous sessions are of course still available (and default) but advanced users who need to store and manage a larger number
of graphs will find new features very useful. A short list of what's new:
- user accounts
- private graph repositories for each user
- repository of public graphs
- graphs can be private or public
- management of private graph repositories
- several new functions in the visualizer: editing, saving, export, ...
- modification of each graph is stored separately so the original query graph is always available
- cloning of public graphs for private use
- ... and plenty of minor updates
13 November 2015
Biomine Explorer graph visualization interface was updated with the latest version of the vis.js
library. There were few minor updates and fixes as well.
15 October 2015
There is a new type of database which contains only data about human: human_16_oct_2015. It is a subset
of the biomine database. However, because it is built separately some nodes and links may differ because of newer data sources.
23 September 2015
Biomine Explorer, Biomine core software and host OS moved to 64-bit and to a much faster machine! This is indeed a huge improvement - process memory limitations on 32-bit systems were causing troubles on every update.
Because of hardware updates user queries should now run much faster. Enjoy!
organism sets were updated so now we have two shiny new databases:
. See Databases
for more info.
13 April 2015
The suggestion input field was modified to accept longer text. This is neccessary if you want to search for certain entities which have very long names
(e.g., potato genes). Also, few new options were added to the advanced graph view (colouring of neighbour nodes and expand option in context menu).
18 February 2015
The advanced graph interface just got nice Bootstrap context menus for nodes and edges! One thing which remains on the todo list is linking to the original data sources.
This will require a little bit of additional work as some of the links are now different as in the original Biomine.
14 January 2015
The Biomine Explorer web search interface got a shiny new query construction area which now also allows to import identifiers from pasted text (in a cute modal window).
13 January 2015
Two new organisms were added to Biomine plants organism set: beet and
cacao. The latest plants database which includes new organisms is called
Also, there was a brief downtime due to a human error and trouble with the database server but everything is
up and working again.
8 January 2015
The updated Biomine and Biomine Explorer are now online!
There is a new web search interface and graph visualization and manipulation plus numerous internal fixes and updates. Please report bugs and comments to
7 January 2015
The first working public set of databases were prepared. The latest are biomine_6_jan_2015 for biomine organism set and
plants_6_jan_2015 for plants organism set.