PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System

bplist00Ò_WebMainResource_WebSubresourcesÕ ^WebResourceURL_WebResourceMIMEType_WebResourceFrameName_WebResourceData_WebResourceTextEncodingName_http://www.phidias.us/index.phpYtext/htmlPOŠt PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System


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Welcome to PHIDIAS! It is a web-based database and analysis system that integrates and analyzes genomic sequences, curated literature information, and gene expression data related to pathogen-host interactions (PHI, or called host-pathogen interactions or HPI). PHIDIAS emphasizes study of those pathogens that cause severe infectious diseases and/or have significant influence in public health.

Core programs in PHIDIAS include:

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Pathogens in PHIDIAS: PHIDAIS currently studies 56 pathogenes, including 24 bacteria, 30 viruses, 1 parasite, and 1 fungus:

#	Bacteria
1	Bacillus anthracis
2	Brucella
3	Burkholderia mallei
4	Burkholderia pseudomallei
5	Campylobacter jejuni
6	Clostridium botulinum
7	Clostridium perfringens
8	Clostridium tetani
9	Coccidioides immitis
10	Corynebacterium diphtheriae
11	Coxiella burnetii
12	Escherichia coli
13	Francisella tularensis
14	Haemophilus influenzae
15	Helicobacter
16	Legionella pneumophila
17	Listeria monocytogenes
18	Mycobacterium tuberculosis
19	Neisseria meningitidis
20	Rickettsia prowazekii
21	Salmonella
22	Shigella
23	Streptococcus pneumoniae
24	Vibrio
25	Yersinia pestis

#	Viruses
1	Crimean-Congo hemorrhagic fever virus
2	Ebola virus
3	Foot-and-mouth disease virus
4	Guanarito virus
5	Hantavirus
6	Hepatitis A virus
7	Hepatitis B virus
8	Human immunodeficiency virus
9	Human papillomavirus
10	Influenza virus
11	Japanese encephalitis virus
12	Junin virus
13	Lake Victoria marburgvirus
14	Lassa virus
15	Louping ill virus
16	Machupo virus
17	Marburg virus
18	Measles virus
19	Mumps virus
20	Poliovirus
21	Rabies virus
22	Reston ebolavirus
23	Rift Valley fever virus
24	Rotavirus
25	Rubella virus
26	Vaccinia virus
27	Varicella-zoster virus
28	Variola virus
29	Venezuelan equine encephalitis virus
30	Yellow fever virus

#	Parasites
1	Plasmodium falciparum

#	Fungi
1	Phakopsora pachyrhizi

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you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // // please send any improvements to aking@internet.com and we'll // roll the best ones in // // adapted from Netscape's Ultimate client-side JavaScript client sniffer // and andy king's sniffer // Revised May 7 99 to add is.nav5up and is.ie5up (see below). (see below). // Revised June 11 99 to add additional props, checks // Revised June 23 99 added screen props - gecko m6 doesn't support yet - abk // converted to var is_ from is object to work everywhere // 990624 - added cookie forms links frames checks - abk // 001031 - ie4 mod 5.0 -> 5. (ie5.5 mididentified - abk) // is_ie4 mod tp work with ie6+ - abk // 001120 - ns6 released, document.layers false, put back in // - is_nav6 test added - abk // 001121 - ns6+ added, used document.getElementById, better test, dom-compl // 010117 - actual version for ie3-5.5 by Michel Plungjan // 010118 - actual version for ns6 by Michel Plungjan // 010217 - netscape 6/mz 6 ie5.5 onload defer bug docs - abk // 011107 - added is_ie6 and is_ie6up variables - dmr // 020128 - added link to netscape's sniffer, on which this is based - abk // updated sniffer for aol4-6, ie5mac = js1.4, TVNavigator, AOLTV, // hotjava // 020131 - cleaned up links, added more links to example object detection // 020131 - a couple small problems with Opera detection. First, when Opera // is set to be compatible with other browsers it will contain their // information in the userAgent strings. Thus, to be sure we have // Opera we should check for it before checking for the other bigs. // (And make sure the others are !opera.) Also corrected a minor // bug in the is_opera6up assignment. // 020214 - Added link for Opera/JS compatibility; added improvements for // windows xp/2000 id in opera and aol 7 id (thanks to Les // Hill, Les.Hill@getronics.com, for the suggestion). // 020531 - Added N6/7 and moz identifiers. // 020605 - Added mozilla guessing, Netscape 7 identification, and cleaner // identification for Netscape 6. (this comment added after code // changes) // 020725 - Added is_gecko. -- dmr // 021205 - Added is_Flash and is_FlashVersion, based on Doc JavaScript code. // Added Opera 7 variables. -- dmr // 021209 - Added aol8. -- dmr // 030110 - Added is_safari, added 1.5 js designation for Opera 7. --dmr // 030128 - Added is_konq, per user suggestion (thanks to Sam Vilain). // Removed duplicate Opera checks left over after last revision. - dmr // 031124 - Added is_fb and version. We report this right after the is_moz // report. - dmr // 040325 - Added is_fx and version. We report this right after the is_moz // report. - dmr // 040421 - Added Debian check to is_moz. Thanks to Patrice Bridoux for // reporting this. // 040517 - Added is_fb/is_fx to plugins based flash detection. Thanks to // Martin Bischoff for pointing out this omission. // 040617 - On Mac IE, appVersion differs from the version in the ua, // with the UA appearing to be more accurate. As an experiment, // for Mac we'll pull is_minor from the ua instead. // // Everything you always wanted to know about your JavaScript client // but were afraid to ask. Creates "is_" variables indicating: // (1) browser vendor: // is_nav, is_ie, is_opera // (2) browser version number: // is_major (integer indicating major version number: 2, 3, 4 ...) // is_minor (float indicating full version number: 2.02, 3.01, 4.04 ...) // (3) browser vendor AND major version number // is_nav2, is_nav3, is_nav4, is_nav4up, is_nav5, is_nav5up, // is_nav6, is_nav6up, is_ie3, is_ie4, is_ie4up, is_ie5up, is_ie6... // (4) JavaScript version number: // is_js (float indicating full JavaScript version number: 1, 1.1, 1.2 ...) // (5) OS platform and version: // is_win, is_win16, is_win32, is_win31, is_win95, is_winnt, is_win98 // is_os2 // is_mac, is_mac68k, is_macppc // is_unix // is_sun, is_sun4, is_sun5, is_suni86 // is_irix, is_irix5, is_irix6 // is_hpux, is_hpux9, is_hpux10 // is_aix, is_aix1, is_aix2, is_aix3, is_aix4 // is_linux, is_sco, is_unixware, is_mpras, is_reliant // is_dec, is_sinix, is_freebsd, is_bsd // is_vms // // based in part on // http://www.mozilla.org/docs/web-developer/sniffer/browser_type.html // The Ultimate JavaScript Client Sniffer // and Andy King's object detection sniffer // // Note: you don't want your Nav4 or IE4 code to "turn off" or // stop working when Nav5 and IE5 (or later) are released, so // in conditional code forks, use is_nav4up ("Nav4 or greater") // and is_ie4up ("IE4 or greater") instead of is_nav4 or is_ie4 // to check version in code which you want to work on future // versions. For DOM tests scripters commonly used the // is_getElementById test, but make sure you test your code as // filter non-compliant browsers (Opera 5-6 for example) as some // browsers return true for this test, and don't fully support // the W3C's DOM1. // // convert all characters to lowercase to simplify testing var agt=navigator.userAgent.toLowerCase(); var appVer = navigator.appVersion.toLowerCase(); // *** BROWSER VERSION *** var is_minor = parseFloat(appVer); var is_major = parseInt(is_minor); var is_opera = (agt.indexOf("opera") != -1); var is_opera2 = (agt.indexOf("opera 2") != -1 || agt.indexOf("opera/2") != -1); var is_opera3 = (agt.indexOf("opera 3") != -1 || agt.indexOf("opera/3") != -1); var is_opera4 = (agt.indexOf("opera 4") != -1 || agt.indexOf("opera/4") != -1); var is_opera5 = (agt.indexOf("opera 5") != -1 || agt.indexOf("opera/5") != -1); var is_opera6 = (agt.indexOf("opera 6") != -1 || agt.indexOf("opera/6") != -1); // new 020128- abk var is_opera7 = (agt.indexOf("opera 7") != -1 || agt.indexOf("opera/7") != -1); // new 021205- dmr var is_opera5up = (is_opera && !is_opera2 && !is_opera3 && !is_opera4); var is_opera6up = (is_opera && !is_opera2 && !is_opera3 && !is_opera4 && !is_opera5); // new020128 var is_opera7up = (is_opera && !is_opera2 && !is_opera3 && !is_opera4 && !is_opera5 && !is_opera6); // new021205 -- dmr // Note: On IE, start of appVersion return 3 or 4 // which supposedly is the version of Netscape it is compatible with. // So we look for the real version further on in the string // And on Mac IE5+, we look for is_minor in the ua; since // it appears to be more accurate than appVersion - 06/17/2004 var is_mac = (agt.indexOf("mac")!=-1); var iePos = appVer.indexOf('msie'); if (iePos !=-1) { if(is_mac) { var iePos = agt.indexOf('msie'); is_minor = parseFloat(agt.substring(iePos+5,agt.indexOf(';',iePos))); } else is_minor = parseFloat(appVer.substring(iePos+5,appVer.indexOf(';',iePos))); is_major = parseInt(is_minor); } // ditto Konqueror var is_konq = false; var kqPos = agt.indexOf('konqueror'); if (kqPos !=-1) { is_konq = true; is_minor = parseFloat(agt.substring(kqPos+10,agt.indexOf(';',kqPos))); is_major = parseInt(is_minor); } var is_getElementById = (document.getElementById) ? "true" : "false"; // 001121-abk var is_getElementsByTagName = (document.getElementsByTagName) ? "true" : "false"; // 001127-abk var is_documentElement = (document.documentElement) ? "true" : "false"; // 001121-abk var is_safari = ((agt.indexOf('safari')!=-1)&&(agt.indexOf('mac')!=-1))?true:false; var is_khtml = (is_safari || is_konq); var is_gecko = ((!is_khtml)&&(navigator.product)&&(navigator.product.toLowerCase()=="gecko"))?true:false; var is_gver = 0; if (is_gecko) is_gver=navigator.productSub; var is_moz = ((agt.indexOf('mozilla/5')!=-1) && (agt.indexOf('spoofer')==-1) && (agt.indexOf('compatible')==-1) && (agt.indexOf('opera')==-1) && (agt.indexOf('webtv')==-1) && (agt.indexOf('hotjava')==-1) && (is_gecko) && ((navigator.vendor=="")||(navigator.vendor=="Mozilla")||(navigator.vendor=="Debian"))); var is_fb = ((agt.indexOf('mozilla/5')!=-1) && (agt.indexOf('spoofer')==-1) && (agt.indexOf('compatible')==-1) && (agt.indexOf('opera')==-1) && (agt.indexOf('webtv')==-1) && (agt.indexOf('hotjava')==-1) && (is_gecko) && (navigator.vendor=="Firebird")); var is_fx = ((agt.indexOf('mozilla/5')!=-1) && (agt.indexOf('spoofer')==-1) && (agt.indexOf('compatible')==-1) && (agt.indexOf('opera')==-1) && (agt.indexOf('webtv')==-1) && (agt.indexOf('hotjava')==-1) && (is_gecko) && (navigator.vendor=="Firefox")); if ((is_moz)||(is_fb)||(is_fx)) { // 032504 - dmr var is_moz_ver = (navigator.vendorSub)?navigator.vendorSub:0; if(!(is_moz_ver)) { is_moz_ver = agt.indexOf('rv:'); is_moz_ver = agt.substring(is_moz_ver+3); is_paren = is_moz_ver.indexOf(')'); is_moz_ver = is_moz_ver.substring(0,is_paren); } is_minor = is_moz_ver; is_major = parseInt(is_moz_ver); } var is_fb_ver = is_moz_ver; var is_fx_ver = is_moz_ver; var is_nav = ((agt.indexOf('mozilla')!=-1) && (agt.indexOf('spoofer')==-1) && (agt.indexOf('compatible') == -1) && (agt.indexOf('opera')==-1) && (agt.indexOf('webtv')==-1) && (agt.indexOf('hotjava')==-1) && (!is_khtml) && (!(is_moz)) && (!is_fb) && (!is_fx)); // Netscape6 is mozilla/5 + Netscape6/6.0!!! // Mozilla/5.0 (Windows; U; Win98; en-US; m18) Gecko/20001108 Netscape6/6.0 // Changed this to use navigator.vendor/vendorSub - dmr 060502 // var nav6Pos = agt.indexOf('netscape6'); // if (nav6Pos !=-1) { if ((navigator.vendor)&& ((navigator.vendor=="Netscape6")||(navigator.vendor=="Netscape"))&& (is_nav)) { is_major = parseInt(navigator.vendorSub); // here we need is_minor as a valid float for testing. We'll // revert to the actual content before printing the result. is_minor = parseFloat(navigator.vendorSub); } var is_nav2 = (is_nav && (is_major == 2)); var is_nav3 = (is_nav && (is_major == 3)); var is_nav4 = (is_nav && (is_major == 4)); var is_nav4up = (is_nav && is_minor >= 4); // changed to is_minor for // consistency - dmr, 011001 var is_navonly = (is_nav && ((agt.indexOf(";nav") != -1) || (agt.indexOf("; nav") != -1)) ); var is_nav6 = (is_nav && is_major==6); // new 010118 mhp var is_nav6up = (is_nav && is_minor >= 6) // new 010118 mhp var is_nav5 = (is_nav && is_major == 5 && !is_nav6); // checked for ns6 var is_nav5up = (is_nav && is_minor >= 5); var is_nav7 = (is_nav && is_major == 7); var is_nav7up = (is_nav && is_minor >= 7); var is_ie = ((iePos!=-1) && (!is_opera) && (!is_khtml)); var is_ie3 = (is_ie && (is_major < 4)); var is_ie4 = (is_ie && is_major == 4); var is_ie4up = (is_ie && is_minor >= 4); var is_ie5 = (is_ie && is_major == 5); var is_ie5up = (is_ie && is_minor >= 5); var is_ie5_5 = (is_ie && (agt.indexOf("msie 5.5") !=-1)); // 020128 new - abk var is_ie5_5up =(is_ie && is_minor >= 5.5); // 020128 new - abk var is_ie6 = (is_ie && is_major == 6); var is_ie6up = (is_ie && is_minor >= 6); // KNOWN BUG: On AOL4, returns false if IE3 is embedded browser // or if this is the first browser window opened. Thus the // variables is_aol, is_aol3, and is_aol4 aren't 100% reliable. var is_aol = (agt.indexOf("aol") != -1); var is_aol3 = (is_aol && is_ie3); var is_aol4 = (is_aol && is_ie4); var is_aol5 = (agt.indexOf("aol 5") != -1); var is_aol6 = (agt.indexOf("aol 6") != -1); var is_aol7 = ((agt.indexOf("aol 7")!=-1) || (agt.indexOf("aol7")!=-1)); var is_aol8 = ((agt.indexOf("aol 8")!=-1) || (agt.indexOf("aol8")!=-1)); var is_webtv = (agt.indexOf("webtv") != -1); // new 020128 - abk var is_TVNavigator = ((agt.indexOf("navio") != -1) || (agt.indexOf("navio_aoltv") != -1)); var is_AOLTV = is_TVNavigator; var is_hotjava = (agt.indexOf("hotjava") != -1); var is_hotjava3 = (is_hotjava && (is_major == 3)); var is_hotjava3up = (is_hotjava && (is_major >= 3)); // end new // *** JAVASCRIPT VERSION CHECK *** // Useful to workaround Nav3 bug in which Nav3 // loads