Try the EPIINFO software, a free download from the CDC website, www.cdc.gov It is a simple and easy software to learn and use, particularly for students. It has built in mapping capabilities to track distribution of infectious diseases and is a robust statistical analysis software designed for epidemiological studies. All the best!
Im not sure if I got the question right. ProMed mail list may be a good tool to track the distribution of an infectious disease. Promed has a website where some tools are availabel to track these reports on maps. http://www.promedmail.org/ However, if the issue is web based softwares for data entry, then OpenClinica is an option. It works similarly as other data entry softwares (EpiInfo, EpiData and CSPro) but it is designed to be installed in a server to allow any one connected to the internet to fill in forms. But different from EpiInfo it has no analysis module.
I know of two such projects of the top of my head. There is Flu Survey, http://flusurvey.org.uk/en/the-project/ which is one of several EU projects tracking voluntary reporting of Influensa. There is also http://healthmap.org/en/ , which plots outbreak reports from the previously mentioned ProMed Mail. Good luck with your course!
For a source of data that is detailed and quite interesting, I recommend the CDC Wonder site, which includes a wealth of up-to-date date on infectious diseases in the U.S. Also, there is a project at the University of Pittsburgh called Project Tycho, which aims to digitize historical epidemiologic data on infectious diseases. The web site is: www.tycho.pitt.edu/
Although there is a lot of time I dont work on this field, some websites of travelers medicine give some updated information about transmissible diseases. HOwever I cant find them right now.
The question asked is indeed a very complex one. We can address aspects of this for a USA community. Firstly, there must be compelling evidence that an infectious disease is indeed present within a defined locale. To determine a base-line presence of specific disease one may go to a CDC model which provides data for locales of distinct geographical side (square miles as an example), different population size, population density, age and sex (include homosexual as a distinct category if disease is a sexually transmitted type), origin of the disease (national vs immigrant component), racial/ethic and environmental criteria if the disease is associated with certain industries (effluent from hospitals, sewers, industrial waste providing culture aspects favoring certain microbial populations, etc). A good deal of this information can be obtained from a local board of health (city and or state or from the CDC). If the disease is of special interest, then specific disease oriented societies are a good source. Secondly, the population components of the given locale must be determined. This can be done by obtaining the most recent USA census report. Once these data are realized, the student must then recruit sources for periodic information. The best way to do this is to establish a TASK FORCE that consists of individuals who have responsibilities relevant to the given disease (hospital infection control committees are an excellent source of expert professionals), local/state health boards, pharmaceutical companies if located close to the site to be monitored, nursing and hygiene personnel of High Schools/colleges/universities within the locale, etc. The Task Force will assist in the development of the needed programme for an epidemiologically based programme.
Lastly, given the novice nature of the lead person involved (University/Master), the results and interpretations should be considered as a "student project" and by no means used as a definitive study. Nevertheless, for diseases within a locale that have been neglected or unsuspected, there is the very good possibility that the stage for a professionally based programme might be established from the data project lead and conducted by the student.