Cytoscape - AOP Xplorer Interaction - aop

I am very vey new at this area. I am trying to be a toxicologist and write my phD thesis on hERG inhibition and long QT syndrome. I have alot of data in terms of literature and shaped it in my mind regarding how to visualize it as an AOP. However, when it comes to do it, my lecturer recommended me to use AOP Xplorer but i couldnt understand how to do it.
Is it possible to visualize my own AOP with regards to my topic via AOP Xplorer (i think so but i need some documents & trainings to understand it)
Could you please give me a hand to understand it properly?
My regards,

It looks like you should be able to visualize your own AOP using AOP Xplorer. If you go to: https://github.com/DataSciBurgoon/aop_networks they have a number of sample networks (look for .sif files). If you construct your data similarly, you should be able to read it in. I've never used that app, however, so your mileage may vary...
-- scooter

Related

Pseudocode system that connects Humans, Devices, and Remote Control

In one scenario, the problem is solved by making pseudocode or actual code that shows a connection between Humans, Devices, and Remote Control.
I'm thinking about doing the ER diagram first and then making it on OOP based. I'm not actually sure what will be the best approach.
Start from the actual UI. UI/UX Prototyping of the features you want for this interaction will help you see what is important and what's not. From there move to the ER diagram.
Creating the ER diagram you should keep in mind what is important for your app's features and how data will be combined together. Also think about the code, no need to write it nor write pseudocode. Just think about it, whether it's possible or not to accomplish a certain demand. In the case you have doubts, write pseudocode to see it through a bit better.
Then, in the end comes the actual study for the exact techstack you're going to use. SQL or NoSQL or both, and the languages different modules and functionalities might need.
Best of luck!!! And also, don't post all your creative ideas on the internet, since other people might steal them ;)

Information about Evolutionary Art

I have begun to do some research about Evolutionary Art algorithm. I read a lot of documents about it. But it seems not easy to understand.
The website http://picbreeder.com is a great example for this. But I don't need this in the beginning because it is too complex.
Where can I find some simple code about this in Java? I think read code could help me much.
Thanks!!!
"Evolutionary Design by Computers" By David Bentley (amazon) has a couple of chapters on evolutionary art. However i dont think it includes any code / pseudocode. The canonical GA should do all you need, however the termination condition could be tricky as art is a subjective subject. (Not objective and therefore enumerable)
Hope this helps...
It looks like the EJC library might help you out, and it looks like a number of open source projects/tools come up if you Google for "java evolutionary computing."
I don't know how simple it is, and believe me it needs to be cleaned up a bit, but I have something that might get you started at https://github.com/murmux/Evo/tree/master/assignment2c It doesn't deal with art, rather game theory, but you can use it under the terms of the GPLv3 if you'd like. That uses Genetic Programming... I have another example using a more vanilla EA I might put up later.
Instead of evolving programs to play "Iterated Prisoner's Dilemma," you would evolve programs to generate an art work. The fun part is coming up with a way to "score" an image for its fitness. (Although Picbreeder seems to skip scoring by having you pick the mating pool directly...)
Check this app: EvoPic, its An evolutionary picture creator that uses Steady-State Genetic Algorithm, to produce evolutionary pictures by drawing uni-code characters in a picture box.
Example:

Correct Approach for mastering SAP R3 and ABAP

I have been working on SAP technology for the last 2.5 years.
As there were so many technical concepts, I couldn't get a single source where I can learn about everything related to it. I didn't get the confidence of mastering all the technical concepts.
Please help me out if you have faced such an experience and how you overcame it.
Suggest some books or a methodology you followed which may be helpful.
Note: I have already worked in Java/J2EE. I am confident enough in mastering the concepts.
Obviously the (or rather a) correct approach would be one that works for you, the conclusion being that you don't know whether the approach was correct until you've tried it. :-)
Enough philosophy - my suggestions would be:
Learn how to read the SAP Online documentation. That's a bit different from reading other documentation - the SAP docs are littered with information about legacy techniques that you don't really need. Learn to identify and skip these parts - you can always come back later.
Develop a knowledge of the data dictionary. It's really at the heart of all things, and if you can't navigate there and read the structures, you're lost. Start reading the chapter in the online docs at http://help.sap.com/saphelp_webas620/helpdata/en/cf/21ea0b446011d189700000e8322d00/frameset.htm.
Read http://help.sap.com/saphelp_webas620/helpdata/EN/fc/eb3138358411d1829f0000e829fbfe/frameset.htm. I know that's a lot of stuff, but it's available for free, and almost everything is in there. Again, do a "fast indexing run" first to get a feeling of what's inside there, then dig into the basic concepts. ABAP at its lowest level isn't fundamentally different from other imperative / procedural languages.
Follow the example programs (transaction code ABAPDOCU). Learn how to use the debugger (vital!) and understand what's going on in the demo programs.
Once you've got a mental model of the basic language, take a look at ABAP Objects. If you already know Java, there should be no problem with the basic concepts, but there are a few specialties.
Feel free to ask if you run into something you don't understand.
There is no single source of information that will provide you with everything you have to know, especially since some of the knowledge is very specific to the context (FI, MM, IS-H, ...).

Understanding code metrics

I recently installed the Eclipse Metrics Plugin and have exported the data for one of our projects.
It's all very good having these nice graphs but I'd really like to understand more in depth what they all mean. The definitions of the metrics only go so far to telling you what it really means.
Does anyone know of any good resources, books, websites, etc, that can help me better understand what all the data means and give an understanding of how to improve the code where necessary?
I'm interested in things like Efferent Coupling, and Cyclomatic Complexity, etc, rather than lines of code or lines per method.
I don't think that code metrics (sometimes referred to as software metrics) provide valuable data in terms of where you can improve.
With code metrics it is sort of nice to see how much code you write in an hour etc., but beyond they tell you nada about the quality of the code written, its documentation and code coverage. They are pretty much a week attempt to measure where you cannot really measure.
Code metrics also discriminate the programmers who solve the harder problems because they obviously managed to code less. Yet they solved the hard issues and a junior programmer whipping out lots of crap code looks good.
Another example for using metrics is the very popular Ohloh. They employ metrics to put a price tag on an opensource project (using number of lines, etc.), which in itself is an attempt which is flawed as hell - as you can imagine.
Having said all that the Wikipedia entry provides some overall insight on the topic, sorry to not answer your question in a more supportive way with a really great website or book, but I bet you got the drift that I am not a huge fan. :)
Something to employ to help you improve would be continuous integration and adhering to some sort of standard when it comes to code, documentation and so on. That is how you can improve. Metrics are just eye candy for meetings - "look we coded that much already".
Update
Ok, well my point being efferent coupling or even cyclomatic complexity can indicate something is wrong - it doesn't have to be wrong though. It can be an indicator to refactor a class but there is no rule of thumb that tells you when.
IMHO a rule such as 500+ lines of code, refactor or the DRY principal are more applicable in most cases. Sometimes it's as simple as that.
I give you that much that since cyclomatic complexity is graphed into a flow chart, it can be an eye opener. But again, use carefully.
In my opinion metrics are an excellent way to find pain points in your codebase. They are very useful also to show your manager why you should spend time improving it.
This is a post I wrote about it: http://blog.jorgef.net/2011/12/metrics-in-brownfield-applications.html
I hope it helps

How to develop *real life* oop skills?

I've been studying OOP for quite a while now and I have a good grasp of the theory. I read the Head First book on OOP and, while it reinforced a lot of the theory, I found the case studies to be somewhat trivial.
I find that I'm applying OOP principles to my code each day, but I'm not sure if I'm applying them correctly. I need to get to the point where I am able to look at my code and know whether I'm using inheritance appropriately, whether my object is cohesive enough, etc.
Does anyone have any good recommendations (books, online guides, blogs, walk-throughs, etc.) for taking the next step in developing solid OOP skills?
I am working primarily in .NET (visual basic), but I welcome suggestions that incorporate various platforms.
Read Refactoring by Martin Fowler, and apply it to your own work.
It will take you through a litany of malodorous characteristics of software code that describe how to detect improperly constructed classes, and even more importantly, how to fix them.
Consider looking into Design Patterns. Although it seems like they aren't commonly used in enterprise applications (I've seen them more commonly used in API's and Frameworks than embedded into enterprise code), they could be applied to make software simpler or more robust in a lot of situations if only developers knew how to apply them.
The key is to understand the design patterns first, then with experience you'll learn how to apply them.
There is a Head First book on design patterns that teaches the concept pretty simply, although if you want a book that really covers design patterns in detail, check out the Gang of Four design patterns book, which is basically what made design patterns mainstream and is referred to almost every time the topic is brought up.
Design patterns can be applied in pretty much any object-oriented language to some degree or another, although some patterns can be overkill or over engineering in some cases.
EDIT:
I also want to add, you should check out the book Code Complete 2. It's a very influential book in the world of software development. It covers a lot of different concepts and theories. I learn something new every time I read it. It's such a good book that if I read it every 6 months to a year, I look at it from a different perspective that makes me a better programmer just by re-reading it. No matter how much you might think you know, this book will make you realize just how little you really know. It's really a great book. I can't stress how much you should own this book.
If you already have the basics, I believe only experience will get you further. You say you are not sure if you are applying the principles correctly, but there is no one correct way. Code you write today, you'll look at in 6 months time, and wonder why you wrote it that way, and probably know of a better, cleaner way of doing it. I also guarantee that after 10 years, you'll still be learning new techniques and tricks. Don't worry too much about it, it will come, just read as much as you can, and try and apply what you read in small chunks.
I am currently half-way through the following book:
http://www.amazon.com/Applying-UML-Patterns-Introduction-Object-Oriented/dp/0131489062
I cannot recommend this book strongly enough in terms of learning a real-life, professional-grade, practical approach to drafting and applying a well-formed and iterative design strategy before diving into code.
I, too, read the "Head First" book and felt that I was much better off for having read it.
After having a few years of working-world experience, I now view the Craig Larman book that I am recommending to be a perfect "next step" for me.
About the Presence of "UML" in this Book Title:
Whether you have positive feelings or negative feelings about UML notation, please do not let that influence your decision to buy the book (ISBN 0131489062) in either direction.
The prominence of "UML" in the title is misleading. While the author does use and explain UML notation, these explanations are extremely well-woven into relevant design discussions, and at no time does this book read like a boring UML spec.
In fact, here is a quote taken directly from the book:
What's important is knowing how to think and design in objects, which is a very different and much more valuable skill than knowing UML notation. While drawing a diagram, we need to answer key questions: What are the responsibilities of the object? Who does it collaborate with? What design patterns should be applied? Far more important than knowing the difference between UML 1.4 and 2.0 !
This book at times seems like it is "speaking to" a lead architect or a project manager. What I mean to say by that is that it assumes that the reader has significant control over the planning and direction of a software project.
Nonetheless, even if you are only responsible for some very small piece of your company's projects and products, I would still recommend this book and encourage you to apply some "scaled down" modifications of the book's advice to your piece of the project.
My OOP epiphany came from Grady Booch's book, way long time ago. Suddenly I realized why objects were good.
While polymorphism is cool, encapsulation is 75% of why objects are cool. It is sort of like an interface: you see the buttons but not the wiring. Before objects, only the most disciplined coders kept their grubby fingers off the internal bits of other people's procedures (it was called "structured programming").
Object make it easy to Do the Right Thing. Inheritance and polymorphism are little bonuses.
One way to learn about objects is to read other peoples' code. I learned a lot by reading the source code for the Delphi VCL framework. Even just looking at the documentation for Java will help you see what a single object class should do and how it is designed to be used by other objects.
Start a project of your own and pay attention when you want to sub-class your own classes and find that you have to go back and break up some protected methods so you can override just one piece of a process instead of replacing all of it. See how ancestors talk to descendants by calling abstract functions. In other words, go make a lot of mistakes and learn from them.
Enjoy!
Frankly, re-reading old David Parnas papers on information hiding helps me get in the right state of mind. The case studies may not be directly applicable but you should be able to get some useful generalizations out of them.
My epiphany happened when I tried to implement a very OO problem (dynamically and recursively building SQL statements) in VB6. The best way to understand polymorphism or inheritance is to need it and not be able to use it.
One thing that will definitely help you is working on a well-known, respected open source project. Either dig through the source code and see how things are done or try to make some additions / modifications. You'll find that there isn't one style or one right answer for most problems, but by looking at several projects, you'll be able to get a wide view of how things can be done. From there, you'll begin to develop your own style and will hopefully make some contributions to open source in the process.
I think you have to attempt and fail at implementing OO solutions. That's how I did it anyway. What I mean by fail is that you end up writing smelly code while successfully delivering a working solution. After it's written you'll get a feel for where things didn't quite feel right. You may have some epiphanies, and/or you may go and hunt for a slicker solution from other programmers. Undoubtedly you'll implement some variation of standard design patterns by accident. In hindsight, a light will click on (oh! so that's what a visitor is for), and then understanding will accelerate.
As others have said, I think tooling through some good OO open source code is a good idea. So is working with more experienced programmers who would be willing to critique your work. However understanding comes through doing.
You might want to try to read (and write) some Smalltalk for a while. Squeak is a free implementation that can show you the power of a fully object-oriented environment (unlike java or .net). All library code source is included. The language itself is incredibly simple. You'll find that java and c# are slowly adding the features well-known to Smalltalk since 1980.
Tortoise HG is extrodanarily well designed piece of OO open source software (written in Python).
If you already understand the basics, building something from scratch in a fully object oriented language will be a good step in fully understanding OOP software architecture. If you don't know Python, Python Essential Reference will take you through the language in full in a few days to a week.
After you understand the language take a look through the software above and you'll have all sorts of epiphanies.
To understand basically anything thoroughly, you need to have a decent knowledge of at least one abstraction level above and one level below it. In the case of OO, others have mentioned design patterns as the layer above OO. This helps a lot to illustrate why OO is useful.
As far as the layer below OO, try to play around with higher-order functions/late binding for a while and get a feel for how these relatively simple constructs are used. Also, try to understand how OO is implemented under the hood (vtables, etc.) and how it can be done in pure C. Once you grok the value of using higher order functions and late binding, you'll quickly realize that OO is just a convenient syntax for passing around a set of related functions and the data they operate on.