About
The MESOCOSM database - for Environmental eXPOsure to nanomaterials Database - is a computational infrastructure for toxicological data management of engineered nanomaterials.
It has developed an environmental exposure database (aquatic mesocosms data, release from products data, ecotox data, …) based on results obtained within the SERENADE's team and H2020 projects.
MESOCOSM aims to predict and explain the nanomaterial behavior and fate in different eocsystems as well as their potential impacts on the environment at different stages of the nanoproducts lifecyle.
In summary, MESOCOSM is a distinct database resource providing thousands of experiment data obtained in tens of unique experiments investigating Ag, CeO2, CuO, TiO2,…-based nanomaterials.
Documentation
Publication
You can find all SERENADE's publications here.
Database file
This the MESOCOSM database schema and this report presents the logical database schema design.
Please refer to the download tab, for additional details about the database installation.
Run application file
This presentation presents the different steps for running the MESOCOSM project
This file contains the executable jar file of the MESOCOSM project.
How to use it?
First copy the folder to your computer and then run the MESOCOSM.jar file.
Once you register, the CEREGE team will send you a username and a password.
Please enter the received Username and Password to launch the project.
For developers, please refer to the download tab, for additional details about the code source.
We hope you are able run these project, if you find any problem just contact the developers:
- Mélanie Auffan
- Jérôme Rose
- Ali Ayadi
Licencing
Licence
The MESOCOSM database and application are free to use under the licence agreement Creative Commons - Share alike.
If you intend to use these database/application, as such or modifying them, please cite this reference :
Ayadi, A., Rose, J., de Garidel-Thoron, C., Hendren, C., Wiesner, M. R., & Auffan, M. (2021). MESOCOSM: A mesocosm database management system for environmental nanosafety. NanoImpact, 21, 100288. doi:10.1016/j.impact.2020.100288
Funding
This work is a contribution to the Labex Serenade (No. ANR-11-LABX-0064) funded by the "Investissements d’avenir" French Government program of the French National Research Agency (ANR) through the A*MIDEX project (No. ANR-11-IDEX-0001-02),
and a contribution to the European Union's Horizon 2020 research and innovation programme under grant agreement No 814426 (NanoInformaTIX).
Download
The MESOCOSM SQL database
The SQL file of the MESOCOSM database can be downloaded here.
Prerequisites
You need a MySQL database server (5.0+) and run the commands below through a user that has the following privileges:
SELECT, INSERT, UPDATE, DELETE,
CREATE, DROP, RELOAD, REFERENCES,
INDEX, ALTER, SHOW DATABASES,
CREATE TEMPORARY TABLES,
LOCK TABLES, EXECUTE, CREATE VIEW
See usage in the MySQL docs.
Installation:
- Download the repository
- Change directory to the repository
Then run/
mysql < EXPOSEDdb.sql
If you want to install with two large partitioned tables, run
mysql < EXPOSEDdb_partitioned.sql
Testing the installation
After installing, you can run one of the following:
Microsoft Windows [version 10.0.17763.914]
(c) 2018 Microsoft Corporation. Tous droits réservés.
C:>cd \xampp\mysql\bin
C:\xampp\mysql\bin>mysql -u (root) -p (password) -h (host server)
Enter password:
Welcome to the Oracle monitor. Commands end with ; or \g.
Your Oracle connection id is 264
Server version: 10.4.6-Oraclem oracle.org binary distribution
Copyright (c) 2000, 2018, Oracle Corporation Ab and others.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
Oracle [(none)]> use serenadedb;
Database changed
Oracle [MESOCOSMdb]> show tables;
+----------------------+
| Tables_in_MESOCOSMdb |
+----------------------+
| bibliography |
| description |
| dictionary |
| experiment |
| institution |
| instrument |
| measure |
| measurement |
| people |
| protocol |
| publication |
| sampling |
| users |
+----------------------+
13 rows in set (0.002 sec)
Oracle [MESOCOSMdb]> describe experiment;
+---------------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+---------------------+--------------+------+-----+---------+----------------+
| IDE | int(200) | NO | PRI | NULL | auto_increment |
| doi | varchar(255) | YES | MUL | NULL | |
| Total_time | int(150) | NO | | NULL | |
| Ecosystem | varchar(20) | NO | | NULL | |
| Primary_consumer | varchar(20) | NO | | NULL | |
| Secondary_consumer | varchar(20) | YES | | NULL | |
| Benthic_inocolum | varchar(20) | YES | | NULL | |
| Planctonic_inocolum | varchar(20) | YES | | NULL | |
+---------------------+--------------+------+-----+---------+----------------+
8 rows in set (0.023 sec)
Oracle [MESOCOSMdb]> describe sampling;
+----------------+-------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+----------------+-------------+------+-----+---------+----------------+
| IDS | int(255) | NO | PRI | NULL | auto_increment |
| IDE | int(255) | NO | MUL | NULL | |
| Injection_mode | varchar(20) | NO | | NULL | |
| Metal | varchar(25) | YES | | NULL | |
| Mineralogy | varchar(25) | YES | | NULL | |
| Shape | varchar(25) | YES | | NULL | |
| Coating | varchar(25) | YES | | NULL | |
| Size | int(25) | YES | | NULL | |
| Contaminant | varchar(25) | YES | | NULL | |
| Sampling_time | int(150) | NO | | NULL | |
+----------------+-------------+------+-----+---------+----------------+
10 rows in set (0.028 sec)
Oracle [MESOCOSMdb]> describe measure;
+----------------------+----------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+----------------------+----------+------+-----+---------+----------------+
| IDM | int(255) | NO | PRI | NULL | auto_increment |
| IDS | int(255) | NO | MUL | NULL | |
| Total_dose | float | NO | | NULL | |
| PH | float | YES | | NULL | |
| Temperature | float | YES | | NULL | |
| Conductivity | float | YES | | NULL | |
| Dissolved_oxygen | float | YES | | NULL | |
| TOC | float | YES | | NULL | |
| ORP_water | float | YES | | NULL | |
| ORP_sediment | float | YES | | NULL | |
| ORP_interface | float | YES | | NULL | |
| Particles_water | float | YES | | NULL | |
| Metal_sediment | float | YES | | NULL | |
| Metal_water | float | YES | | NULL | |
| Dissolved_Metal | float | YES | | NULL | |
| Metal_layings | float | YES | | NULL | |
| Metal_gland | float | YES | | NULL | |
| Metal_adult | float | YES | | NULL | |
| Metal_juveniles | float | YES | | NULL | |
| CU_NI_sediment | float | YES | | NULL | |
| Speciation_digestive | float | YES | | NULL | |
| Speciation_layings | float | YES | | NULL | |
| Speciation_juveniles | float | YES | | NULL | |
| Adult | float | YES | | NULL | |
| Juveniles | float | YES | | NULL | |
| Picoplankton | float | YES | | NULL | |
| Picobenthos | float | YES | | NULL | |
| Algae_water | float | YES | | NULL | |
| Algae_sediment | float | YES | | NULL | |
| TBARS | float | YES | | NULL | |
| TAOC | float | YES | | NULL | |
+----------------------+----------+------+-----+---------+----------------+
31 rows in set (0.029 sec)
Oracle [MESOCOSMdb]> describe publication;
+-----------------+--------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-----------------+--------------+------+-----+---------+-------+
| DOI | varchar(350) | NO | PRI | NULL | |
| Title | varchar(250) | YES | | NULL | |
| Journal | varchar(250) | YES | | NULL | |
| Year | varchar(250) | YES | | NULL | |
| Volume | varchar(250) | YES | | NULL | |
| Issue | varchar(250) | YES | | NULL | |
| Page | varchar(250) | YES | | NULL | |
| Contact_Author | varchar(250) | NO | | NULL | |
| Keywords | varchar(250) | YES | | NULL | |
| Abstract | varchar(250) | YES | | NULL | |
| Publish_Status | varchar(250) | YES | | NULL | |
| Curation_Status | varchar(250) | YES | | NULL | |
| Curation_Note | varchar(250) | YES | | NULL | |
+-----------------+--------------+------+-----+---------+-------+
13 rows in set (0.027 sec)
Oracle [MESOCOSMdb]> describe publication;
+-----------------+--------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-----------------+--------------+------+-----+---------+-------+
| DOI | varchar(350) | NO | PRI | NULL | |
| Title | varchar(250) | YES | | NULL | |
| Journal | varchar(250) | YES | | NULL | |
| Year | varchar(250) | YES | | NULL | |
| Volume | varchar(250) | YES | | NULL | |
| Issue | varchar(250) | YES | | NULL | |
| Page | varchar(250) | YES | | NULL | |
| Contact_Author | varchar(250) | NO | | NULL | |
| Keywords | varchar(250) | YES | | NULL | |
| Abstract | varchar(250) | YES | | NULL | |
| Publish_Status | varchar(250) | YES | | NULL | |
| Curation_Status | varchar(250) | YES | | NULL | |
| Curation_Note | varchar(250) | YES | | NULL | |
+-----------------+--------------+------+-----+---------+-------+
13 rows in set (0.027 sec)
Oracle [MESOCOSMdb]> describe bibliography;
+-----------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+-----------------+--------------+------+-----+---------+----------------+
| Bibliography_ID | int(250) | NO | PRI | NULL | auto_increment |
| People_ID | int(250) | NO | MUL | NULL | |
| Institution_ID | int(250) | NO | MUL | NULL | |
| DOI | varchar(350) | NO | MUL | NULL | |
+-----------------+--------------+------+-----+---------+----------------+
4 rows in set (0.025 sec)
Oracle [MESOCOSMdb]> describe description;
+----------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+----------------+--------------+------+-----+---------+----------------+
| Description_ID | int(255) | NO | PRI | NULL | auto_increment |
| Table_descrip | varchar(250) | YES | | NULL | |
| Field | varchar(250) | YES | | NULL | |
| Note | varchar(250) | YES | | NULL | |
| Data_type | varchar(250) | YES | | NULL | |
| Valid_value | varchar(250) | YES | | NULL | |
+----------------+--------------+------+-----+---------+----------------+
6 rows in set (0.029 sec)
Oracle [MESOCOSMdb]> describe dictionary;
+---------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+---------------+--------------+------+-----+---------+----------------+
| Dictionary_ID | int(255) | NO | PRI | NULL | auto_increment |
| Group | varchar(250) | YES | | NULL | |
| Item | varchar(250) | YES | | NULL | |
| Parameter | varchar(350) | YES | | NULL | |
+---------------+--------------+------+-----+---------+----------------+
4 rows in set (0.024 sec)
Oracle [MESOCOSMdb]> describe institution;
+----------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+----------------+--------------+------+-----+---------+----------------+
| Institution_ID | int(255) | NO | PRI | NULL | auto_increment |
| Department | varchar(250) | YES | | NULL | |
| Institution | varchar(250) | YES | | NULL | |
| City | varchar(250) | YES | | NULL | |
| State | varchar(250) | YES | | NULL | |
| Zipcode | varchar(250) | YES | | NULL | |
| Country | varchar(250) | YES | | NULL | |
+----------------+--------------+------+-----+---------+----------------+
7 rows in set (0.042 sec)
Oracle [MESOCOSMdb]> describe people;
+-------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+-------------+--------------+------+-----+---------+----------------+
| People_ID | int(255) | NO | PRI | NULL | auto_increment |
| First_Name | varchar(250) | YES | | NULL | |
| Last_Name | varchar(250) | YES | | NULL | |
| Middle_Name | varchar(250) | YES | | NULL | |
| Email | varchar(250) | YES | | NULL | |
| Phone | varchar(250) | YES | | NULL | |
| Web | varchar(250) | YES | | NULL | |
+-------------+--------------+------+-----+---------+----------------+
7 rows in set (0.021 sec)
Oracle [MESOCOSMdb]> describe instrument;
+----------------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+----------------------+--------------+------+-----+---------+----------------+
| Instrument_ID | int(255) | NO | PRI | NULL | auto_increment |
| Name | varchar(250) | YES | | NULL | |
| Model | varchar(250) | YES | | NULL | |
| Manufacturer_Name | varchar(250) | YES | | NULL | |
| Manufacturer_City | varchar(250) | YES | | NULL | |
| Manufacturer_State | varchar(250) | YES | | NULL | |
| Manufacturer_Country | varchar(250) | YES | | NULL | |
+----------------------+--------------+------+-----+---------+----------------+
7 rows in set (0.025 sec)
Oracle [MESOCOSMdb]> describe protocol;
+----------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+----------------+--------------+------+-----+---------+----------------+
| Protocol_ID | int(255) | NO | PRI | NULL | auto_increment |
| Name | varchar(250) | YES | | NULL | |
| Duration_Value | int(250) | YES | | NULL | |
| Duration_Units | varchar(250) | YES | | NULL | |
| Description | varchar(250) | YES | | NULL | |
| Reference | varchar(250) | YES | | NULL | |
+----------------+--------------+------+-----+---------+----------------+
6 rows in set (0.027 sec)
Oracle [MESOCOSMdb]> describe users;
+----------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+----------+--------------+------+-----+---------+----------------+
| id | int(150) | NO | PRI | NULL | auto_increment |
| username | varchar(200) | NO | | NULL | |
| password | varchar(200) | NO | | NULL | |
+----------+--------------+------+-----+---------+----------------+
3 rows in set (0.019 sec)
JAVA Graphical User Interface (GUI)
It allows managing with the MESOCOSM SQL database via a DataBase Management System (DBMS).
Download file
The source code is freely downloaded at here .
Prerequisites
You need:
- A java 8.0 or Higher version must be installed.
- An OS windows 10, Mac or any version of Linux.
Source code
It contains all the source code that means all java files.
How to use it?
Firts donwload Netbeans from http://netbeans.org/downloads/index.html;
After the installation of Netbeans start netbeans and go to File Menu;
Open project and navigate to Source Code_Netbeans folder;
In the library add all the jar files which is given in the lib folder;
And run the porject.
EXPOSED.exe
It is executable EXE of our Project, just double click it and install in any directory.
Some time it creats problem when you intall this software in C:\ drive, due to some admin rights to Write data in Database so its better to install in other drive.
Contact us