Monitoring Humidity and Temperature in Biological Collections Using Free Software Tools Herson Esquivel Vargas Instituto Nacional de Biodiversidad (INBio) Costa Rica hesquivel@inbio.ac.cr Rev 3.0 Eng Abstract The useful life of biological collections depends on the quality of preventive maintenance applied. Using informatics tools to track humidity and temperature facilitates maintenance and should be considered essential for high sensitivity collections. This paper presents an automated solution for monitoring humidity and temperature using free software and low cost hardware, applicable among other areas, to biological collections. This solution was successfully implemented at INBio, but it go for other biological collections in any institution. Keywords: web, humidity, temperature, monitoring, sensor, biological collection. 1. Introduction The importance of biological collections lies in harnessing that scientific community can make of it. They provide primary data that could be used in many subsequent investigations, also, are essential because they constitute the historical physical evidence on which many publications are generated over time. Given the importance of biological collections for the scientific community and society in general, it is necessary to ensure the satisfactory preservation of all the specimens[1], to be transmitted to future generations in the best possible conditions [2]. There are physical, biological and chemical agents that may influence the preservation of a collection. Environmental physical agents such as humidity and temperature directly impact the appearance of deteriorating biological agents. Proper control of these variables permits to make better decisions related to preventive maintenance of the collection. Fungus and insecticides are examples of biological and chemical deteriorating agents, respectively. 2. Related Projects There are different solutions on the market for monitoring humidity and temperature with appliances with pluggable sensors in a modular way and even with a web visualization interface. Among the main disadvantages encountered is the cost, as the main appliance may cost more than $1,000 USD and each one of the sensors must be of the same brand with an average cost of $200 USD. Another disadvantage found is that the hardware manufacturer is the sole provider of software for the system, so updates are arbitrary [12]. Among its positive aspects is that the installation and implementation of the system can be achieved in a shorter time as there is not need of any server installation. Other lower-cost products also allow the recording of humidity and temperature data with a display in the same place where they are located but do not have historical data or a web interface to query data, implying that someone is responsible for making registration [11]. 3. Architecture - Hardware The proposed system consists of several components interconnected with computer networks. A simplified diagram is shown in Figure 1. In the lower part is presented the core of
the system, responsible for the gathering of data sent by the sensor; the database server, which preserves the information in a consistent manner; and the web server, that provides a simple interface to view data. These three components can be located on a single physical server, or be distributed across multiple servers as illustrated in Figure 1. The minimum hardware requirements for the server will depend on the number of sensors and clients that the system must support. Figure 1: Architecture of the system In the upper left side of Figure 1 is the sensor that has two main tasks: 1) take readings of environmental data 2) transmit it across the network to the core. For this reason, the sensor actually consists of two specialized elements for each task: a sensor itself, on charge of the first task, and a computer to connect the sensor to the Ethernet LAN (IEEE 802.3) or WLAN (IEEE 802.11), to make the second task. For simplicity was chosen a sensor with USB interface that only has the basic capabilities of data reporting, although on the market are available some with additional features such as alarms and display in-situ of data [13]. Finally, on the upper right side of Figure 1 is located the client which makes data queries in a web application. The web server might or not be published on the Internet. Software and hardware modularity, permits interchange and update of different components without a major impact in the overall system. It is not required new high performance hardware, instead, is an opportunity to use obsolete equipment or systems with a low workload. 4. Software All software used on the different components of the system uses GNU/GPL or compatible licenses, so, it is free (libre) and allows continuous, sustainable and fair improvement. The cost of using the software is only the installation process, and if required, custom module development. 4.1. Sensor The computer that is part of the sensor must meet two basic software requirements: SSH service and the driver responsible for controlling the USB connected sensor. Also, it is required to download/write a plug-in to make readings using the driver, and should meet the guidelines for the development of Nagios [4]. Most part of GNU/Linux systems, includes the SSH service by default and the main problem is the driver installation because manufacturers usually do not provide it for free operating systems. In spite of this, a lot of drivers of different hardware can be found on Internet with the source code available for improvement and adaptation to the needs. Additional software might be running if hardware features are good enough. 4.2. Server-side The core of the system is a monitoring software called Icinga (a Nagios project fork) [5]. This software is traditionally used to monitor servers, printers and other network connected devices, but in fact it is able to monitor virtually anything. The server receives the reports and place them in one of three categories: Ok, Warning or Critical. The database server could be MySQL or PostgreSQL, thanks to a software component called ido2db that maintains the independence of the core engine system with a specific Database Management System.
Apache with the PHP module is the web-server on charge of the execution of the web application of data visualization. Additionally, you can consider installing an SMTP server to send notifications by e-mail to the persons responsible for preventive maintenance of the monitored area. 4.3. Client The only software needed is a web browser compliant with basic standards. The client must have a user name and password to access the application that lets him remotely observe the data reported. You can create different profiles for different people to isolate sensor data reports, accordingly to the people's work area. 5. Implementation In the case of the implementation done at INBio, TEMPerHUM sensor was used with acceptable results and low cost (Figure 2) [7]. Figure 2: TEMPerHUM - Dimensions: 59 x 17 x 6mm Moreover, to connect the sensor, it was decided to use a plug-computer [3], which brings factoryinstalled the Ubuntu operating system. Its dimensions are 55 x 77 x 41.5 mm, which makes it very attractive to place it anywhere in the collection. It has a power consumption of 13W, -that is lower than a traditional PC- [8]. The Sheeva-Plug computer (Figure 3) used has one USB port that can connect a USB Hub to add devices such as memories, web-cams, LEDs and water sensors, among others. The connection between the plug-computer and the core system, is via wired Ethernet network, although some models also offer the possibility of wireless connection. Thanks to the little space they occupy the sensor and the computer, they can be placed in any space of the room considered relevant for data collection, even, within the shelves, using USB extensions. The USB sensor used, has a factory driver designed for Windows operating system, so it was needed the implementation of another driver for the Sheeva-Plug's Ubuntu operating system. The source code of the driver and plug-in is available at INBio's subversion server svn://pulsatrix.inbio.ac.cr/temper_hum/ The system is configured to take samples every 5 minutes and to save historic data. In INBio were used virtual servers in a distributed setup, using the stable version of Debian GNU/Linux operating system. For this particular implementation, which already has the server, the cost of the USB sensor and the Sheeva-Plug computer is less than $130 USD, a reason for which it is considered a feasible option for government offices, NGOs and museums with limited budgets, guarding biological collections. 6. Results During the early days of implementation were performed tasks of testing and calibration of the sensor, according with other traditional sensors already installed in the collection. In Figure 4 is shown a chart of 288 samples taken during July 11 th, 2010, starting at 00:00 and finishing at 23:59. The yellow line represents the percentage of relative humidity and the blue line the temperature in degrees Celsius. Vertical axis represents humidity and temperature. Figure 3: Sheeva-Plug [10] Photo by: Chievery
23:15 20:40 18:05 15:30 12:55 10:20 07:45 05:10 02:35 00:00 Temperature / humidity 80.00 70.00 60.00 50.00 40.00 30.00 20.00 10.00 0.00 Figure 4: Chart of samples Over several days you can see trends and relationships between changes in humidity and temperature changes. Between 11:00 and 15:00 hours is usually seen a drop in relative humidity as temperature increases, however, between 04:00 and 06:00 hours can be seen an humidity increase, proportional to the temperature. The first experimental data shows an average temperature between 20.05 C and 64.4% of relative humidity. It has also been a good performance and correct operation of all components of the system with a 24 / 7 workload. 7. Future work Temperature and humidity Collection #1 - July 11th, 2010 Hour RH% Temp C The project lends itself to be extended with different features that may be desirable depending on application area. This deployment will be extended to send email and SMS notifications, so that manual verification is considered a good practice but not a daily requirement. Another of the most needed requirements is data plotting, since the current version makes a textual report which is difficult to read in macro-level. It is under evaluation the RGraph library [9], which takes advantage of HTML5 and the JavaScript language to plot the information on the client side. Remote handling of air conditioners and dehumidifiers is also considered desirable, when they provide digital control interfaces, so they can be handled by the same computer which connected the sensors, through commands sent via the web. 8. Conclusions This is an interdisciplinary project, which may involve personal of computer engineering and industrial maintenance (responsible for maintaining the ideal conditions of humidity and temperature). Also, is easily expandable with a combination of hardware + software efficient and inexpensive. A basic setup would consist of the following steps: a) Download the Icinga software [5]. b) Install on a server: MySQL, Apache and Icinga. c) Install the sensor to the plug-computer or another computer available. d) Configure the core system to receive data from sensors. The system facilitates a continuous remote monitoring of temperature and relative humidity thanks to the web interface which avoids a person having to be physically in front of the collection display, and writing manually the data report in a log. With the analysis of the results is expected that the collections, with invaluable scientific importance, have a better preventive maintenance and hence a longer useful life. It is also expected a reduction in spending power by turning on dehumidifiers and air conditioning equipment during the periods with most favorable rates. References [1] Mesa Ramírez, Diana Paola, Protocolos para la preservación y manejo de colecciones biológicas. Boletín Científico, Museo de Historia Natural Vol. 10, enero diciembre. Págs.
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