An interactive Web-Based database of antibiotic resistance in bacteria in aquaculture systems: structure.

Transcription

1 A iteractive Web-Based database of atibiotic resistace i bacteria i aquaculture systems: structure. M. Giacomii, R. Michelii, 2 S. Bertoe, F. Raffo, C. Ruggiero Abstract Dept. of Commuicatio Computer ad System Sciece Uiversity of Geova Via Opera Pia Geova Italy Mauro.Giacomii@dist.uige.it 2 RI.L.A.B. srl Via Guerrazzi 24/2 646 Geova Italy. The iteret is the fastest growig tool ad arguably the most popular method of accessig public domai iformatio. Web-based applicatios will ot oly eable people to take advatage of the wide geographic coverage ad low cost of the iteret, but will also save time, moey ad traiig i the future as trasitio to a browser-based user iterface stadard cotiues. The preseted applicatio has bee desiged i order to collect data comig from aquaculture samples. It is part of the Europea fouded project ASIARESIST (ICA4-CT ). This project aims to isolate bacteria resistat to atibiotics i fish water ad sedimet samples comig from Malaysia, Thailad ad Vietam. We preset the techical choices ad specific implemetatio of the database ad its iterface. The fial result of this system will be a steadily growig database moitorig atibiotic treds ad dyamics across the idustry ad the eviromet of the south-east Asia regio. Keywords: Database; Active Server Pages; Aquaculture; Data access; Flash; Iteret; Atibiotics. Itroductio The iteret is the fastest growig tool ad arguably the most popular method of accessig public domai iformatio. This New World has become a iteractive eviromet where server, cliet, various devices ad users are iteractig at differet levels, sharig software ad busiess services. Oe applicatio area with great promise is web access to data. Usig the iteret brigs the beefit of fast ad itelliget data access ad data storig to a whole ew audiece, opeig up ew possibilities for data sharig. Web-based applicatios will ot oly eable people to take advatage of the wide geographic coverage ad low cost of the iteret, but will also save time, moey ad traiig i the future as trasitio to a browser-based user iterface stadard cotiues. Whe choosig a architecture for a data storig ad retrieval applicatio, the desiger has to face a umber of issues that really guide or focus the developmet process. A cliet/server side applicatio should be easy to develop, scale, maitai, deploy ad use. A primary cosideratio i plaig is idetifyig who will use the Web applicatio: the audiece. The Web applicatio s audiece ca be defied by idetifyig those who have access to the Web applicatio ad idetifyig the type of Web browser they use. The capabilities of the Web browser also shape the plas for usig cliet ad server script i the Web applicatio. Usig server script ad Active Server Pages (ASP), browser- idepedet pages ca be easily geerated. The server processes the server script ad the seds HTML to the browser. I cotrast, if the type of browser that the user

2 has is kow, cliet scripts ca be used to geerate the page ad miimize the load o the server. Whatever implemetatio strategy is chose for the cliet/server applicatio, security must be cosidered. Data should leave the cliet ad reach the server beig safely protected from hacker s access. Commoly used methods to idetify a user are: cookies, user-id ad password or IP umbers. This web-based applicatio has bee desiged i order to collect data comig from aquaculture samples. It is part of the Europea fouded project ASIARESIST (Hazard aalysis of atibiotic resistace associated with Asia aquacultural eviromets - ICA4- CT INCO-DEV Program). ASIARESIST aims to isolate bacteria resistat to atibiotics i fish water ad sedimet samples comig from Malaysia, Thailad ad Vietam. 2. Materials ad Methods This web based applicatio has bee desiged to collect data comig from biological samplig o fishes ad their eviromet comig from three differet coutries: Malaysia, Thailad ad Vietam. The mai poits we focused o were: Programmig laguages Database structure Cotrollig data access User iterface 2. Cliet server architecture This architecture is based o the iteractio of two computers to perform a task. The cliet requests the iformatio eeded to the server, which seds it back to the cliet. The Iteret is based o a cliet server model. I that case the server is a Web Server. It is a computer cotaiig all the web pages of a web site. The cliet is a web browser, which receives the HTML pages set by the server ad shows it o the user scree []. I our applicatio the web server resides i the Bioegieerig ad Medical Iformatics laboratory of DIST (MedIfo - DIST - Uiversity of Geova) while all the other parters play the part of the cliets coectig to it every time they have ew samples to store ito the database. To avoid problems related to cliet scripts (differet type of browser ad differet versios of browser software) we used oly server-side scriptig implemeted usig Active Server Pages. 2.2 Active Server Pages Active Server Pages (ASP) eables Hypertext Markup Laguage (HTML) authors ad Web developers to mix HTML ad ilie scriptig usig ay authorig tool. The scripts ca referece compoets ruig o the local server or ay other server to access databases, applicatios or process iformatio. Whe a browser requests a.asp file, the web page is processed by the server ad it is retured to the cliet as plai HTML (fig.). ASP is a server side scriptig laguage, which exists oly o the server ad caot be visible to the cliets. For this reaso ASP provides a browser idepedet approach to applicatio desig [2].

3 Active Server Pages program code ca be writte usig differet scriptig laguages such as VBScript, Jscript or PerlScript [3]. We chose to use VBScript as its sytax is similar to Visual Basic laguage ad our group was already familiar with that laguage. 2.3 Microsoft Access Database Fig. : ASP/HTML process Microsoft Access has built a traditio of iovatio by makig historically difficult database techology accessible to busiess users i geeral. Whether users are coected by a LAN, the Iteret, or ot at all, Microsoft Access esures that the beefits of usig a database ca be quickly realized. With its itegrated techologies, Microsoft Access is desiged to make it easy for all users to fid aswers, share timely iformatio, ad build faster solutios. At the same time, Microsoft Access has a powerful database egie ad a robust programmig laguage, makig it suitable for may types of complex database applicatios. We orgaised a powerful relatioal database ready to host data comig from the project. 2.4 User recogitio There are three mai ways of recogisig a user coected to a web site: Cookies User-id ad password IP address Cookies are text files of small sizes that are set by the Web server ad stored o the computer of the user. These files ca cotai various iformatio such as a user id or a password ad they ca be read o certai evets to retrieve user s iformatio. The mai problems related with cookies are that the web server idetifies a computer ad ot a user ad that the user ca delete the cookie from the hard disk becomig uidetifiable durig the ext access. The IP address is a umber give by the provider of the iteret coectio to the computer that is coected to the etwork. IP addresses ca be static or dyamic. A IP umber is static whe it does ot chage i time, that meas that the computer has always the same IP address. O the other had the IP umber is dyamic whe the provider gives the computer a differet umber each time the computer eters the etwork. Oce agai IP umber does

4 ot idetify the user but oly the computer coected to the server ad if the computer has a dyamic IP address it caot be recogised at all. The best way to recogise a user ad to limit access to the web site is to assig each user a user ID ad a password. The server will keep a copy of them i a database or i a text file ad will allow the user to eter the web site oly if the oe iserted matches with the stored oe. At first we decided to avoid uexpected access to the web server by opeig the access oly to the IP umbers of the project s parters. We the discovered that i most cases their IP umber was assiged dyamically ad may of the Asia parters could ot access the database. For this reaso we decided to use oce agai the database for storig a user ID ad a password for each of them. 2.5 User iterface A key factor i developig a web applicatio is its purpose. After havig clearly specified the Web applicatio s purpose the features ad fuctios that defie the visitor s experiece ca be easily determied. Oe of the most commo thigs oe wats to do i a dyamic Web applicatio is to iteract with a user; this is commoly accomplished usig the forms ad fuctios provided withi HTML. Tags are iserted ito the HTML text to provide cotrols o the Web page. Usig forms is a effective way of gettig iformatio from a user ad passig it to aother page for further iteractio or to a database for recordig purposes [4]. Our database has bee desiged to host data describig: Samplig site Fish farm Samplig period Sample descriptio Each parter should isert data of samples comig from three differet sites i his home coutry ad belogig to three differet types of sample: water, sedimet ad orgaism. As the amout of data is high ad it is easy to get cofused, we thought it would have bee better to add some visual help to our parters by the use of Flash itegrated with ASP ad HTML. 3. Results The aim of the Italia participatio i the Asiaresist project is to build a Web based applicatio made of a HTML graphical iterface ad a database residig o a web server for a easy isertio ad maiteace of data comig from aquaculture samples. The first part of the project is cocered with obtaiig a collectio of atibiotic resistat bacterial isolates derived from aquaculture sites of ecoomic importace i Malaysia, Thailad ad Vietam. Each bacteria is the classified o the base of its coutry of origi, the farm i which the sample has bee take, ad the type of samplig medium i which it has bee isolated. There are three types of samplig medium for each farm: water, sedimet ad orgaism. At the ed of the process of isolatio, each parter gets 44 isolates from the three samplig sites chose for his coutry. O the basis of data isertio ad accordig to a Stadard Operatig Procedure for samplig agreed amog all parters, followed by us i the creatio of the database, each strai is give a code, which cotais iformatio about:

5 Resistace / No resistace to a certai cocetratio of atibiotic Coutry of origi Samplig Site Fish farm pod Samplig period Sample type Coloy umber All the iformatio is stored i the relatioal database, together with the strai code. I order to avoid excessive maipulatio of data, each parter has the right of isertig data oly ito the database related to his/her coutry but oce iserted, they ca oly be deleted by the database admiistrators. The overall structure of the database is show i fig. 2 accordig to the Etity-Relatio otificatio [5]. COUNTRY HAS FARM CONTAINS LIVE BREED POND PERSON SPECIES TREAT WATER COLLECT FROM SAMPLE SEDIMENT ISOLATE STRAIN Fig.2 Etity-Relatio diagram. To obtai that ad to avoid exteral access to data, the first page of the web site is a logi page askig for a USER ID ad a PASSWORD. The user is allowed to eter oly if the iserted data matches with the oes i the USER table of the database. This method allows the server to recogise a user ad to give him/her certai rights over data, for example the admiistrator ca access data deletio pages, while the other users ca oly access data isertio pages with coutry restrictios. At the release the User database cotais oly the resposible of each coutry, so that they are the oly authorised persos to access the database. They ca authorise other persos, but oly for maipulatig data of his/her coutry. Oce the bacterial strai isolatio is completed, Atibiotic Susceptibility Test is

6 performed. This test idicates susceptibility of the orgaism to the atibiotic beig tested by a clear zoe of ihibited growth aroud the impregated filter discs. Due to the itrisic visual ature of this testig we decided to develop a program with Macromedia Flash MX, which resembles the dishes used i the experimets. Flash is a excellet tool for iteractive applicatio developmet i iteret. It uses vector graphics, everythig you see o your scree is displayed by a mathematical calculatio, meaig that a Flash movie ca stretch to fit ay resolutio ad still look good (as log as you do't have ay raster graphics such as jpegs i it), which has always bee a huge barrier for HTML. Each atibiotic (white circles) becomes a butto. Oce it is clicked it chages its colour to red ad the user is asked to isert growth diameter ad other data about the testig. Whe all data have bee iserted ad stored ito database, the image will chage to show the growth ihibitio diameters previously iserted. A B 4. Coclusios Fig. 3: Atibiotic Susceptibility Test iput form (A empty - B partially filled) The preset paper presets a applicatio that jois together database, server-side scripts ad HTML graphical iterface ito a comprehesive data storig system. The system has bee desiged i order to provide a user friedly iterface for data isertio ad a powerful relatioal database which, by the ed of the project, will become a publicly accessible database for atibiotic resistace moitorig of evirometal bacteria. This system has bee desiged to improve data iterchage by the use of a stadard commuicatio protocol ad by the settig up of commo user friedly iterfaces, i order to optimise the efficiecy of data maagemet. The fial result of this system will be a steadily buildig database moitorig atibiotic treds ad dyamics across the idustry ad the eviromet of the south-east Asia regio. 5. Ackowledgemet This work is partially supported by the project ASIARESIST (Hazard aalysis of atibiotic resistace associated with Asia aquacultural eviromets - ICA4-CT INCO-DEV Program), fuded by Europea Uio. We are grateful to our Asiaresist Parters i the Aquatic Aimal Health Research Istitute (Thailad), Ca tho Uiversity (Vietam), Uiversity of Ghet (Belgium), Uiversity Putra Malaysia (Malaysia) ad Uiversity of Stirlig (UK) for their agreemet to this publicatio, ad for their support.

7 6. Refereces [] Darell R. HTML 4 Uleashed. Macmilla Computer Publishig, 997. [2] Scott M, Atkiso J. Active Server Pages 3.0. Macmilla Computer Publishig, [3] Goodma D. JavaScript Bible,4 th Editio. The McGraw-Hill Compaies, 200. [4] Crouch R, Amudse M. Database Programmig with Visual IterDev 6 i 2 Days. Sams Publishig,999. [5] Batii C, Ceri S, Navathe SB. Coceptual database desig. Redwood City, CA USA: The Bejami/Cummigs Publishig Compay Ic., 992