I have a aligned BAM file which I want to simulate to generate reads. The platform I used is Ion AmpliSeq Whole Exome Sequencing. I want to know if there are any read simulators for Ion Torrent platform.
Look at this publication:
Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data, Caboche et al. BMC Genomics, 2014, 15:264.
Their tool is CuReSim, never used it yet, but I will try it.
Maybe it can help you...
Related
I am making an EEG bio-feedback'product' for a friend and I need a simple but DSP-powerful application builder.
Here is my situation:
I have built the HW to measure the brainwave signals and need to create a user panel for my friend to use it. The HW sends a stream of ascii out a serial port. The data packets send the amplitude value at a rate of 250 packets per second. Brain waves of interest are below 30 HZ so this is more than fast enough sampling.
I am prototyping the DSP user panel in LabVIEW which makes it incredibly easy to do sophisticated DSP with a custom control panel. However, my friend just wants a plug and play product and I can hardly install LabVIEW on his PC, so here is my challenge: I am wondering if there is a design application that I can use to create the final application for him.
I have no problem if it is text based but I don't have the capacity to sit down with a full-on programming language to make the front panel controls, internal DSP and serial port processor, so the application would hopefully provide the designer easy to tool-up GUI and easy to access DSP library. I am up to coding stuff to interpret the serial data format and manage the general flow of the data to get it processed and sent to the front panel, but all the fussy details of setting up some programming IDE and installing a bunch of libraries to make the front panel is more than I can take on right now.
BTW, I also put this together in a private edition of Matlab but again that is no good for my friend.
Any ideas? I know there are high-level application builders around but they usually target beginners. I am so spoiled by Labview! I have no problem with the actual coding like in C, Basic, or maybe Python, it's all the environment-building I don't want to get pulled into.
If you want a stand alone executable, you can use LabVIEW's application builder to create one. The app builder ships with LV pro, but can be purchased separately for cheaper versions. This won't let your friend modify the code, but I understand that's what you want.
There are also numerous ways to create plugin systems, if that's needed in your case. You can find various tutorials on that.
Be aware that some toolkits and modules require that you purchase distribution licenses as well. You would need to check whether you're using such a module.
We need to visualize BP (business process) into BPMN, but NOT by hands using modeler. We need to do it automatically in crm-web-based system written on PHP. I have input data (etc. array, xml, not care...(but not BPEL)), then I need to process it into nice BPMN graph (using SVG).
We have first nice-looking realization of it. We use matrix to draw: several times goes through matrix and optimize graph each time, no no, it working fast, but it not agile, hard to rebuilt, upgrade, add new features... We made this algorithm by ourselves (I mean we didn't find it in google or books). Problem is that we couldn't find any algorithms in the internet. I suppose we don't know correct keywords to do it. Every try returned us to BPEL vis. from BPMN, "Data flow vis." returned modelers...
Please help us to find some algorithms, or give correct keywords to find out information.
Think you're probably looking for "graph layout algorithms". The only library I'm aware of that can (I think) generate BPMN directly is the yFiles library from yWorks. It's not free. They do however offer a free application using the library that does auto-layout. Perhaps you could do some prototyping with that.
If that's not applicable, there are several other options. I'm not aware any of these can generate BPMN symbols directly; you'd have to construct the symbols. However all will auto-layout graphs according to various algorithms. Also all open source/free.
graphviz. Written in C. Quite old now but well used, stable and scalable.
tulip. Newer than graphviz. Haven't used it but heard good things about flexibility and scalability.
see also this post for javascript based options.
There are many more, just google for graph layout algorithms / libraries.
hth.
I have been trying to make work EZSIM with no luck, which is a software to build discrete event simulators in a graphical DOS environment. In this software, my simulator and many others (of the other people in the course I'm taking) don't work, but teacher's simulator (and examples of the downloaded files) does work.
So, I began to distrust of the software.
Do you know any software that resolves the same kind of problems but really works? It will be good if it is free, or I can download an evaluation copy or something like that.
If you don't know any software, do you know any library which might work? Preferably in C#, Ansi C, Java or Delphi.
This may be more than what you're looking for, but check out NS2. It's the standard for open source network simulations, and will allow you to simulate all kinds of network layer behavior.
I've also used JUNG in the past. It's very flexible, although it also doesn't offer much out of the box.
I used Möbius in my computer systems analysis class. It is free for educational use (which sounds like what you're doing). It's a Java GUI which generates C++ code.
The R package queuecomputer. queuecomputer is a computationally efficient method for simulating queues with arbitrary arrival and service times. There is a submitted paper on arXiv describing the algorithm used in the package. Examples can be found within the arXiv paper and the vignette. A web app based on the package is available at https://ace-ebert.shinyapps.io/queue_simulator_mmk/ .
There is what seems to be a plethora of version control systems. Therefore, to draw a bad conclusion, it must be easy to write one.
What are some issues that must be considered in order to write a simple file versioning system? (What are the minimum necessary functions?)
Is it a feasible task for one person?
A good place to learn about version control is Eric Sink's Weblog. His most recent article is Time and Space Tradeoffs in Version Control Storage, for one example.
Another good example is his series of articles Source Control HOWTO. Yes, it's all about how to use source control, but it has a lot of information about the decisions and tradeoffs developers have to make when designing the system. The best example of this is probably his article on Repositories, where he explains different methods of storing versions. I really learned a lot from this series.
How simple?
You could arguably write a version control system with a single-line shell script, upversion.sh:
cp $WORKING_COPY $REPO/$(date +"%s")
For large binary assets, that is basically all you need! It could be improved quite easily, say by making the version folders read-only, perhaps recording metadata with each version (you could have a text file at $REPO/$(date...).meta for example)
That sounds like a huge simplification, but it's not far of the asset-management-systems many film post-production facilities use (for example)
You really need to know what you wish to version, and why..
With large-binary assets (video, say), you need to focus on tools to visually compare versions. You also probably need to deal with dependancies ("I need image123.jpg and video321.avi to generate this image")
With code, you need to focus on things like making diff's between any two versions really easy. Also since edits to source-code are usually small (a few characters from a project with many thousands of lines), it would be horribly inefficient to copy the entire project for each version - so you only store the differences between each version (delta encoding).
To version a database, you probably want to store information on the schema, tracking new tables, or columns, or adjustments to existing ones (rather than calculating deltas of the database files, or making copies like the previous two systems)
There's no perfect way to version everything, you have to focus on doing one thing well.. Git is great for text, but not for binary files. Adobe Version Cue is great with binary files (images), but useless for text..
I suppose the things to consider can be summarised as..
What do you want to version?
Why can I not use (or extend/modify) an existing system?
How will I track differences between versions? (entire files? deltas?)
What other data do I need to attach to versions? (Author? Time-stamp? Dependancies?)
What tasks would a user commonly need to do (diff'ing? reverting specific files?)
Have a look in the question "core concepts" about (D)VCS.
In short, writing a VCS would involve making a decisions about each of these core concepts (Central vs. Distributed, linear vs. DAG, file centric vs. repository centric, ...)
Not a "quick" project, I believe ;)
If you're Linus Torvalds, you can write something like Git in a month.
But "a version control system" is such a vague and stretchable concept, that your question is really unanswerable.
I'd consider asking yourself what you want to achieve (learn about VCS, learn a language, ...) and then define some clear goal. It's good to have a project, but it's also good to have a reachable goal in a small amount of time. Small successes are good for your morale.
That IS really a bad conclusion. My personal opinion here is that the problem domain is so wide and generally hard that nobody has gotten it "right" yet, thus people try to solve it over and over again, from different angles and under different assumptions.That of course doesn't mean you shouldn't try. Just be warned that many smart people were there before you, so you should do your homework.
What could give you a good overview in a less technical manner is The Git Parable.
It is a nice abstraction on the principles of git, but it gives a very good understanding what a VCS should be able to perform. All things beyond this are rather "low-level" decisions.
A good delta algorithm, good compression and network efficiency.
A simple one is doable by one person for a learning opportunity. One issue you might consider is how to efficiently store plain text deltas. A very popular delta format is the one from RCS (used by many version control programs). You might want to study it to get ideas.
To write a proof of concept, you probably could pull it off, implementing or borrowing the tools Alan mentions.
IMHO, the most important aspect of a VCS is ease-of-use. This sounds like an odd statement, but when you think about it, hard drive space is one of the easiest IT commodities to scale horizontally, so bad compression or even real sloppy deltas are going to be tolerated. The main reason people demand improvement in versioning systems is to do common tasks more intuitively or to support more features that droves of people eventually demand but that weren't obvious before release. And since versioning tools tend to be monolithic and thoroughly integrated at a company, the cost to switch is high, and it may not be possible to support a new feature without breaking an existing repo.
The very minimal necessary prerequisite is an exhaustive and accurate test suite. Nobody (including you) will want to use your new system unless you can demonstrate that it works, reliably and completely error free.
I don't just mean publish, but pretty much everything between when the pure coding is finished and the first version is released. For example, how do games make it so that their save files are hidden/unhackable, how do they include their resources within the game as opposed to having a resource file containing all of the sprites, etc., how do they make it so that there are special file extensions like .rect and .screen_mode, and so on and so forth.
So does anyone know any good books, articles, websites, etc. that explain the process between completing the pure code for a game and the release of it?
I don't think developers make much of an effort to ensure saves are hidden or unhackable. PC games usually just save out to a folder, one file per save, and any obfuscation is likely the result of using a binary file format (which requires some level of effort to reverse-engineer) or plaintext values that aren't very meaningful out of context, but not deliberate attempts to circumvent hacking. There are probably a ton of PC games that have shipped with very easily hackable text or XML save files, but I've never been a save hacker so I don't have any specific examples. On consoles the save files are going to a memory card or the console's hard drive, which makes them inherently inconvenient to access, but beyond that I don't think console developers make much of an effort to encrypt or otherwise obfuscate save data. That energy would more likely be directed towards securing the game against cheating if it's on online game or just making other systems work better.
Special file extensions come from just using your own extensions and/or defining your own file formats. You can use any extension for any file, so there are tons of "special" file formats that are just text files with a different extension, I've done this plenty of times myself. In other cases, if they have defined their own binary file format, that means they also have their own file parsers to process those files at runtime.
I don't know what platforms you have in mind, but for PC and console games, resources are not embedded in the executable. You will generally see a separate executable and then various archives and configuration files. Depending on the game, it may be a single resource pack, or perhaps a handful of packs for related resources like graphics, sound, level data, etc. As a general observation console games are more aggressively archived (to minimize file operations on slow optical media, and perhaps to overcome limitations of the native file systems on more primitive platforms). Some PC games have very loose assets, with even script files hanging out in the open.
If you develop for Windows or XBox 360, Microsoft might offer some help here. Check out their Game Development tools for Visual Studio C++ Express Edition.
If you are looking for books the Game Development Essentials series should answer your questions.
For circumventing saved file modifications, you can implement a simple encryption algorithm and use it to encrypt saved files, and then decrypt them when loading. File extensions are simply a matter of choice.
To use special file extensions in your game, just do the following:
Create some files in a format of your choice that have that extension, and then
write some code that knows how to read that format, and point it at those files.
File extensions are conventions, nothing more; there's nothing magic about them.
ETA: As for embedding resources, there are a few different ways to approach that problem. One common technique is to keep all your resources bundled together in a small number of files - maybe only one (Guild Wars takes that approach).
At the other extreme, you can leave your resources spread across many files in a directory tree, maybe in a custom format that requires special tools to modify, and maybe not. Civilization 4 does things this way, as do all the Turbine games I'm familiar with. This is a matter of taste, and not very important either way.
I think a better solution is two break your images in tiles of some known size and then join them back to back in some random order in a new file. This random order is only known to you and hence only you know how to jumble the tiles to get the original image back.
The approach would be to maintain a single dimensional array and maintains the position of tiles in it. Know use the crop functions of MIDP to extract each tile and render each tile back to the console.
If you need, I can post the code for you.
I would suggest to check the presentation from the developers of World of Goo (great game):
http://2dboy.com/public/eyawtkagibwata.pdf.