BioWebApps: A collection of applications for Biologists from around the web.
Bioinformatics
- JalView 2
Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.
- Sequence Manipulation Suite 2
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.
- SeWeR 3
SeWeR is an acronym, stands for SEquence analysis using WEb Resources. In addition to its common *dirty* use, the word SeWeR also has two meanings- first, "a medieval servant or household officer of high rank in charge of serving dishes at the table and sometimes of seating and tasting" and the second one, "one who sews". SeWeR fits all of these definitions. First, it is *dirty* at the code level. Second, it serves. It serves you a single door to all the common web-based services for sequence analysis. And it sews. It sews all these services together. For a refined mind, SeWeR is an integrated portal to common web-based services in bioinformatics.
Ecology
- Woods
Woods simulates northeastern U.S. forest growth with 3 tree species. Features disruptions (hurricanes, deer grazing, fires, etc.), landscape fragmentation, and mixed site quality. Woods is primarily a teaching simulator, used at a number of universities. Java 1.3.
- GrassWorld
GrassWorld models a 3-level grassland food chain: plant, grasshopper, and grasshopper-hunting spiders. Optional competing plant species. Java 1.3.
- ScaredyWorld
ScaredyWorld is a GrassWorld model where herbivores can hide from predators, at a cost. Java 1.3.
Genetics
- Mendel's Peas
Interactive Tutorial/Simulation that uses Mendel's famous breeding experiments with peas to review meiosis and its consequences and to review simple pedigree analyses.
Other
- JFDraw
JFDraw is a pure Java based graphics application and library package. JFDraw uses features of Java2D and expanded graphic routines for more complex vector drawings. JFDraw is focused on vector graph drawing field. It can help you to complete your mechanical, electronic, architectural graphs drawing applications, or even business process or workflow graphs issues.
- FoilSim II
With this software you can investigate how an aircraft wing produces lift by changing the values of different factors that affect lift. There are several different versions of FoilSim II which require different levels of experience with the package, knowledge of aerodynamics, and computer technology. This web page contains the on-line student version of the program. Additional versions of the program and hyperlinks to pages in the Beginner's Guide to Aerodynamics are available from the developers website.
- JavaFoil
JavaFoil is a relatively simple program, which uses several traditional methods for airfoil analysis. The following two methods build the backbone of the program:
- The potential flow analysis is done with a higher order panel method (linear varying vorticity distribution). Taking a set of airfoil coordinates, it calculates the local, inviscid flow velocity along the surface of the airfoil for any desired angle of attack.
- The boundary layer analysis module steps along the upper and the lower surfaces of the airfoil, starting at the stagnation point. It solves a set of differential equations to find the various boundary layer parameters. It is a so called integral method.
