Stuart Ray's Pile of Links Back to my home page

Please note my disclaimer at the bottom of this page. In particular, this is just a list of links that I find personally useful and/or interesting. Inclusion does not represent an endorsement of anything for any purpose. I do not have time to systematically check that the links work, nor that they continue to point where they once did.

Johns Hopkins Medicine

Dept of Medicine Home Page
- Viral Hepatitis Center
- Johns Hopkins Antibiotic Guide
- Johns Hopkins Infectious Diseases Service
- Johns Hopkins AIDS Service
- MNet - Computer network services
- Osler Medical Journal - the online journal of the Osler Medical Service, JHH
- OslerNet- the Intranet for the Osler Medical Service, Johns Hopkins Hospital
- Arthritis
- Cardiomyopathy Service
- Vasculitis
- Online Mendelian Inheritance in Man (OMIM) - an extremely valuable search tool
- Johns Hopkins Saturday Medicine Rounds
- The Kelly G. Ripken Program - info for patients with Grave disease
Graduate programs
- Immunology

MSTP (MD/PhD) program

Intranet
- Infectious Diseases Intranet
- Inside Hopkins Medicine
  - Broadcast emails
  - Graphical Standards - for stationery, sites, etc.
  - JHU Licensing and Technology Development - for MTAs, etc.
- Professorial promotions
- Science Calendar
- Infonet: JH Med Inst Information Network - the "old" JHH intranet
Finding people:
- LDAP search - search the old JHMI LDAP
- Text pagers - Internal only
Dermatlas - a large repository of well-documented dermatological images
JHED - the Johns Hopkins Medicine Enterprise directory
- JHEM - iPlanet email server
- iPlanet calendar
- JHEM status
Hopkins Medicine - the JHH Internet portal
- School of Medicine
- HopkinsTelemedicine - telemedicine at Hopkins
DNA Analysis Facility - sequencing, synthesis, and other solutions on CMSC 10
- Finch
Office of Medical Informatics in Education - resources and links for innovative approaches
Pathology Data Systems at Johns Hopkins Hospital - Home of LabWeb
Pharmacy: JHH Formulary
JHMCIS homepage - a HUGE site with a variety of resources
- Micromedix - info for providers and patients
- Electronic Patient Record - info and downloads
- RxWriter
WelchWeb - William H. Welch Medical Library
- Welch Classes and Instruction
- JHMI Macintosh Users Group Home Page
NTS Web - the IT site for JHMI
- Antivirus site
- JHMI-Net email status

Johns Hopkins University top

JHUNIVERSE: Johns Hopkins University on the Web - the JHU home page
- AT&T ISP info - information about special deals with JHU's preferred Internet Service Provider
Purchasing
- Contract list
JHED - the Johns Hopkins University Enterprise Directory
Homewood Academic Computing home
- Software - it is amazing what academic discounts can do for software prices
- JHU Mailing Lists - creating, managing and using
Welcome to The JHU Book Center - a place to get stuff at academic prices
JHU E-Mail Centralized Name Registration - where I got shortened to "sray@jhu.edu"

Maryland top

Maryland Recycles - Old computers should not just be discarded. Here is another option
List of Servers (USA - Maryland)
MD Mass Transit Administration (MTA) - Light rail, Metro, bus, MARC

Medical top

Infectious Diseases stuff

CDC Home Page - not just MMWR - also treatment guides, surveill summaries...
- Epi Info Home Page - you can learn about and download it from the CDC site
- MMWR - Why pay for subscription when you can get it free here?
- How to Obtain Birth, Death, Marriage, and Divorce Certificates
- Emerging Infectious Diseases
World Health Organization - a more global perspective on health
- Weekly Epidemiological Record - just as the name implies, with a global view
Institute for Molecular Virology - a very readable site with tons of info on viruses
Infectious Diseases Society of America - membership and job info
ICD-9 Codes - Infectious and Parasitic Diseases - courtesy of the AAFP
Infectious Diseases Links - maintained at King/Drew Health Sciences Library
I.D.-related guidelines from the American Heart Association
- Antibiotic Treatment of Endocarditis (1995)
- Prevention of Bacterial Endocarditis (1997)
Medical Management of Biological Casualties - the USAMRIID "Blue Book"

Online versions of print resources & Searching

PubMed at the NLM - free MedLine searching!
Free Medical Journals - 'nuff said?
FreeBooks4Doctors - self-explanatory
ProCite and Reference Manager by RIS - examples of citation management software
Institute for Scientific Information (ISI): Science Citation Index and Current Contents
- Journal Citation Reports
- Web of Science (IP authentication or login)
American College of Physicians - the dominant professional organization for Internists
American Medical Association
Infectious Diseases Society of America
- Clinical Infectious Diseases
- Journal of Infectious Diseases
Journal of Virology - the BEST virology journal (IMHO)
New England Journal of Medicine - CPCs in full, plus abstracts and some images
Science - the journal, from the AAAS homepage

Research (see also HCV and HIV research below)

NIH Home Page - lots of research-related information
- National Institutes of Health -- Grants and Contracts
- CRISP - for searching the NIH funded projects database
- NIH Study Sections - rosters, contact info, etc
- PHS 398 forms - in Acrobat PDF format
- PHS 398 instructions - in HTML format
dbGaP - a NLM database for linking Genotype and Phenotype
GrantsNet - grant info, esp for young investigators
American Type Culture Collection Home Page - cell lines and the like
Scirus - a search engine for science
Research Ethics - page I created for instruction of Immunology graduate students

Medical education

JHU Ofc of Medical Informatics in Education - resources & links for innov approaches
AAMC: GEA SIGs: Computers in Medical Education Special Interest Group
Interactive Patient - an educational simulation
The Medical Education Page - Greg Allen (MSII) created a nice resource on the WWW

Other medical resources

Amer Assoc for Therapeutic Humor - humor is important to a therapeutic relationship
Medscape - a bit too unfocused for my tastes, but well done visually
Virtual Hospital - very polished visually
BONES (tm) The Biomedically Oriented Navigator of Electronic Services )
The National Library of Medicine - lots of old medical stuff
ABIM - the American Board of Internal Medicine
MedicineNet Pharmacy
HIPAA resources - "administrative simplification" [hah!]
DICOM - the medical imaging graphical standard
ICD-9 codes - a list available from Duke University
MedAl - the Medical Algorithms Project

HCV top

Professional Organizations

AASLD - Americal Association for the Study of Liver Diseases
EASL - European Association for the Study of the Liver

Meetings

The Liver Meeting (AASLD) - in Boston (27-31 Oct, 2006)
HCV meeting 2006 - in Cairns, Australia (27 Aug - 1 Sep)

Research resources

HCV database at LANL - Another excellent free resource from our friends in New Mexico
- PhyloPlace - very nice tool for 'placing' a HCV sequence
RNS HCV Database - HCV sequence database and analysis tools (France) [1 month lag from EMBL]
HCV sequence server - great resource for HCV sequence data (Japan) [variable lag from DDBJ, 5 months as of 16 Sept 2001]
Taxonomy browser at NCBI

General info

Johns Hopkins Viral Hepatitis Center - the Johns Hopkins Infectious Disease Service site
From the CDC:
- Hepatitis info
- MMWR RR19 (pdf version) Prevention and Control of Hepatitis C Virus
Viral Hepatitis - Tulane Univ. course notes
Hepatitis Central - a well-crafted, voluminous site created by someone infected with HCV
Hepatitis C Forum - a German site (English language pages), also by someone with HCV
Hepatitis C Foundation - lots of information, though the advertising for dietary supplements and unproven therapies is a little distracting

HIV/AIDS - General top

Meetings

CROI - the Conference on Retroviruses and Opportunistic Infections

Research stuff - Retrovirology

Simplot - Windows program I created for analyzing sequences for mosaicism
RAP_Links - David Robertson's Links to Recombinant sequence Analysis/detection Programs
HIV Sequence Database WWW Home Page - incredible resource
- Reference Alignments
KTL - Mika Salminen's lab at National Public Health Institute, Helsinki
NIH AIDS Research and Reference Reagent Program
The_ANRS_at_Marseille - a European site devoted to the study of HIV
AmFAR (American Foundation for AIDS Research) - an important funding source
Institute for Molecular Virology - great stuff about virology in general as well as...
HIV Protease Database - basic science, not how to prescribe or take PIs
Retrosearch - for studying endogenous retroviruses (a slow-loading database with lots of info)

General/clinical stuff

Johns Hopkins AIDS Service - a resource for providers of care
Stanford HIV mutation analysis - nice interface
Global Programme on AIDS - World Health Organization - great statistics and graphics
UNAIDS
HIV/AIDS Treatment Information Service
Library of Images - some useful images for teaching about HIV
Yahoo! - Health:Diseases and Conditions:AIDS/HIV
The Body: As to Treatment Qs - archived Q&A; Joel Gallant now answers Qs here
HIV | InSite - another site for AIDS care providers (not as good as ours, of course)
CDC Daily AIDS Summaries (gopher)
ASD Online - WHO site for AIDS and STDs
USCA Website Index Page
HIVpositive.com - info for the lay reader

Human genome

Genome database - the international consortium
Celera academic offerings - a more commercial side of human genome project

Immunovirology top

Current Protocols in Immunology - available only from the JHMI campus
Immunology Council - a JHU program
Epitope prediction tools

IEDB - Immune Epitope Dabase and Analysis Resource
Parker algorithm - Dr. Kenneth Parker's algorithm for predicting HLA binding epitopes
Rammensee algorithm - a.k.a. SYFPEITHI, another algorithm for epitope prediction
EpiPred - prediction of epitopes using spreadsheets
EpiPredict - prediction of MHC class II-respected epitopes
JenPep
ProPred - prediction of HLA-DR binding regions

Epitope Motifs - from the HIV Immunology database at Los Alamos, based on the Rammensee motif database
IMGT/HLA Database - part of the international ImMunoGeneTics project
FIMM - functional immunology database
MHCBN - a database of MHC binding (and non-binding) peptides
SImmune - software for modeling systems (e.g. signalling)

Straight virology

"All the Virology on the WWW" - the title may be over-the-top, but the content IS good, including the Big Picture Book
- don't miss: Weird Virology on the WWW
The Institute for Molecular Virology - not as deep on virology as the above, but GREAT visuals
American Society for Virology
Introduction to Molecular Virology - self-explanatory, many nice areas
Pan-American Society for Clinical Virology
Viral Genomes at NCBI

Molecular phylogeny/sequence analysis top

Software (all are available at no cost, except for PAUP*)
- BioEdit - a fantastic and free sequence editor, written by Tom Hall
- Clustal - the de facto standard in desktop sequence alignment
  - Clustal home page (home to ClustalW and ClustalX)
  - ClustalX version 1
- Description of Software - at the Marine Biology Lab: Workshop on Molecular Evolution
- FigTree - A graphical viewer for phylogenetic trees
- HyPhy - Hypothesis testing using Phylogenetic analysis
- JAligner - a Java implementation of Smith-Waterman alignment
- Mega - a nice integrated analysis program
- ModelTest - David Posada's excellent tool for identifying a best-fit model using PAUP*
- MrBayes - phylogenetic analysis using Bayesian inference
- MrModelTest - a model testing program and other tools from Johan Nylander
- MrMTgui - a GUI for ModelTest and MrModelTest
- PAML - Ziheng Yang's Phylogenetic Analysis by Maximum Likelihood
- PAUP* - phylogenetic analysis using parsimony, also ML and other methods (not free)
- PHYLIP Home Page - Home page of Joe Felsenstein's PHYLogeny Inference Package
  - PHYLIP download Page - anonymous ftp page for PHYLIP
- Phylogeny Programs - A nice jumping point for info and downloads
- Tree-Puzzle - Maximum likelihood analysis (formerly "Puzzle")
- TreeView - a REALLY great program for manipulating trees
- WebLogo 3 - a fantastic logo generator (web app and downloadable Python source)
Online tools
- At the LANL databases:
  - FindModel - online tool for selecting a phylogenetic model
  - TreeMaker - online tool for making a quick NJ tree
- Bioinformatics at IGBMC - a wealth of analysis tools in France
- Pictogram - web server at MIT - can only do DNA
- NCBI tools
  - ORF Finder
  - OMIM - Online Mendelian Inheritance in Man
- PBIL - Pôle Bioinformatique Lyonnais
Molecular Databases
- NCBI Home Page - Where you will find tools to view and submit sequence data
- National Center for Genome Resources
- European Molecular Biology Laboratory
- PDB WWW Home Page
- GSDB Sequence Excerpt Retrieval Tool
- The Institute for Genomic Research
The Tree of Life - Somewhat addictive, a wonderful concept
Macintosh Molecular Evolution Software - ditto
Biotechnology Software server at the University of Indiana - ditto
Primer on Molecular Genetics (Department of Energy)
Codon Usage Database

Molecular Biology top

Current Protocols in Molecular Biology - available only from the JHMI campus
Molecular Biology Gateway - lots of links
Primer3 - a site at MIT for PCR primer selection, with good documentation
The BioCatalog - an amazing wealth of software for biological scientists
Codon Usage Database - located in Japan, based on work by Prof. Toshimichi Ikemura
NWFSC Molecular Biology Protocols
English-French MolBiol dictionary (gopher)
REBASE - the definitive database of restriction enzymes, and it's free!
NIH Image - proof that free software can set standards of excellence
RNA Folding Software
DNA Express - not an endorsement, but this is one place to get oligos made

General Science

ChartAll - generates charts from your data, flexible and free!
Searching for chemical structures
- Chemical compound tree at WikiCommons
- Chemspider
NIST Exploratory data analysis
Graphing calculators:
- GCalc - a very full-featured Java solution
- GraphIt - an educational Java applet
- GraphCalc - a full-featured free Windows application
- PowerCalc - Microsoft's solution (download link listed on this page)

Borland Delphi^® Programming - what a joy! top

Borland Delphi Home Page
- Borland Community
Delphi Developer's Guide - a great Delphi book
Magazines for Delphi developers
- Delphi Informant
- The Delphi Magazine - soon to disappear, sadly!
Raize Software - developer tools, makers of Raize Components, CodeSite, etc.
- CodeSiteEx - and other CodeSite-related tools from Rick Ackerson
Steema - makers of TeeChart and other components
Delphi Super Page
TurboPower - [former] makers of Systools, Sleuth QA Suite, etc [now open-source projects]
XN resource editor (free)
UnicodeStrings in D2009
Alt codes - codes for entering special characters using the Alt key in Windows

Palm^®top

Palm home page
- Palm Healthcare Solutions
Security applications for your handheld - for encrypting lists of passwords, account #s, etc
These applications sync with a user-friendly desktop application
- Cloak - from the makers of PocketMirror
- SplashID - excellent interface
- TealLock - from a highly reputable company
Acrobat Reader for PalmOS - who'd have thought?
PilotGear H.Q.
PalmPilotFiles - formerly Ray's Palmpilot Software Archive
Pilot Programming FAQ - formerly "Wade's ..."
Teal - a dizzying array of high-quality software, etc.

Unix/Sun/Solaris^®resources top

Just plain good/interesting/whatever top

Entertainment/Culture
- xkcd - funniest comics on the 'net (for geeks like me, anyway)
- PhD comics - hard on PIs like me, also uncomfortably close to the truth (!)
- The Loh Life - Caltech grad with insightful and funning musings
- Bartlett's Familiar Quotations
- Classics at the Online Literature Library
- Folk Music Search
- Shakespeare
- Poets & Writers, Inc. - Home Page
- Spirograph - takes me back...
Hoaxes/urban legends (look here before you forward that email...)
- Hoaxbusters at CIAC
MS Sharepoint resources
- Robert Shelton's blog
- Nikhil's blog
- MSDN virtual labs -a training "sandbox"
- Form deployment
Information
- Wikipedia - an amazing, participatory, free resource!
- ISI Web of Knowledge - go to Web of Science to search for lit cited
- IANI country code lookup - for two-letter country codes
- MapQuest - for maps and directions
- CIA World Factbook - an amazing wealth of maps and information
- Your Nation - cool way to look at demographic data, etc.
- NPR Programs
- The University Pages - find academics anywhere! - great site!
- SKY Online - Your Astronomy Source on the World Wide Web
- Astronomy pic of the Day - GREAT space pictures, with excellent explanations
- Light Pollution Awareness - the links page is excellent
- Ripe NCC - reverse IP lookup
- ZIP code lookup - from the US Postal Service
- WordIQ - definitions, etc.
- PopClocks - US and World population clocks
Practical
- USNO Official Time
- About French language
- How to Link to the NCBI Citation Matcher - to incorporate live citations into HTML
- US State Department - Services - Passports
Encyclopedias
- Britannica online - just not the same as the old leather-bound version
- Wikipedia
  - Wikipedia template filler - for citations
Wordle - totally cool way to display text

Travel / Leisure

Search for fares
- Expedia
- Farechase
- FareCompare
- Hotwire
- Kayak
- Mobissimo
- Priceline
- Qixo
- SideStep
- Travelocity
Amtrak - my favorite way to travel
Traffic resources
- CHART - Maryland traffic maps and cameras
- Traffic.com - Free but requires registration
Airlines - why just these? No good reason.
- American
- Southwest
- United
- US Airways
Wine spectator - searchable wine guide

Weather top

WeatherNet
Wunderground.com - worth the $5 per year, in my opinion
NCDC - National Climatic Data Center
TropMet - wide variety of tropical weather resources
- Tropmet Images - amazing photos and videos from hurricanes
Tutiempo - historical weather data, worldwide!

Back to my home page

This page is the sole responsibility of Stuart Ray, and does not necessarily reflect the opinions or policies of the Johns Hopkins University. Inclusion of links to commercial sites does not constitute endorsement by me or JHU of any goods or services, but does suggest that I found the site interesting for some reason. Or maybe it slipped in by accident. Note: if you are a human (i.e. not a spammer) trying to reach me, please remove "nospam" from my address.

updated 16 February 2009