Optimus | Workflow for LC-MS feature analysis and spatial mapping

by MolecularCartography Python Version: v1.5.1 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | Optimus Summary

Optimus is a Python library. Optimus has no bugs, it has no vulnerabilities and it has low support. However Optimus build file is not available and it has a Non-SPDX License. You can download it from GitHub.

Optimus is a workflow for LC-MS-based untargeted metabolomics. It can be used for feature detection, quantification, filtering (e.g. removing background features), annotation, normalization and, finally, for spatial mapping of detected molecular features in 2D and 3D using the `ili app. Optimus employes the state-of-the-art LC-MS feature detection and quantification algorithms by OpenMS which are joined into a handy pipeline with a modern workflow management software KNIME with additional features implemented by us. The workflow is being developed by Alexandrov Team at EMBL Heidelberg (contact information) in collaboration with the Dorrestein Lab at UCSD.

Support

Quality

Security

License

Reuse

Support

Optimus has a low active ecosystem.

It has 11 star(s) with 9 fork(s). There are 11 watchers for this library.

It had no major release in the last 12 months.

There are 5 open issues and 6 have been closed. On average issues are closed in 74 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of Optimus is v1.5.1

Quality

Optimus has no bugs reported.

Security

Optimus has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

Optimus has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

Optimus releases are available to install and integrate.

Optimus has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions are available. Examples and code snippets are not available.

Top functions reviewed by kandi - BETA

kandi has reviewed Optimus and discovered the below as its top functions. This is intended to give you an instant insight into Optimus implemented functionality, and help decide if they suit your requirements.

Convert source file to csv format
Find file with given file descriptor .
Check if the given GitHub response has the given status code .

Get all kandi verified functions for this library.

Optimus Key Features

No Key Features are available at this moment for Optimus.

Optimus Examples and Code Snippets

No Code Snippets are available at this moment for Optimus.

Community Discussions

Trending Discussions on Optimus

Changing default focused screen on awesome wm

How to get value from JSON format

Problem "WebGL is not supported by your browser" in Rmarkdown

NoClassDefFoundError: com/couchbase/client/java/error/TemporaryFailureException

Datatables only returns last row on select event

Unknown error: Error: No valid exports main found for src\main\ui\node_modules\uuid?

Hashtable: Only saving the last element added

Gtk/gtkmm glarea queue render doesnt work with dedicated graphics

Laravel Policy Id Obfuscation

Detect gzip encoding to manually decompress response, but 'Content-Encoding' header missing

QUESTION

Changing default focused screen on awesome wm

Asked 2021-Mar-22 at 17:47

I have a bit of a hacky setup on my laptop where I use optimus-manager to configure my screen layout at X startup based on whether an external monitor is connected or not. If it is, I only want to use the external monitor and not the laptop monitor, but because of a limitation of NVIDIA drivers, I need to leave my laptop monitor on, and just lower the backlight brightness. See my /etc/optimus-manager/xsetup-hybrid.sh for how this works (eDP-1 is my laptop screen, and HDMI-1-0 is my external monitor):

...

ANSWER

Answered 2021-Mar-19 at 21:07

It's likely apps are being displayed where the mouse currently resides. You could use xdotool to ensure mouse is on desired display to begin with.

Source https://stackoverflow.com/questions/66687389

QUESTION

How to get value from JSON format

Asked 2021-Mar-03 at 09:42

I am using Python request module to get API response. The response is should be JSON format. From the response how do I retrieve the specific value?

Example of API response:

...

ANSWER

Answered 2021-Mar-01 at 10:37

change this:

Source https://stackoverflow.com/questions/66420471

QUESTION

Problem "WebGL is not supported by your browser" in Rmarkdown

Asked 2021-Jan-11 at 11:14

I'm using Knit to PDF in Rstudio for a Rnotebook containing 3D graph generated by plotly. Then in the PDF,

When I click on the link, I have

I'm using Rstudio 1.3.1093.0 on Windows NT 10.0.19042. In my GPU Diagnostics report, I have

...

ANSWER

Answered 2021-Jan-11 at 11:14

I don't think you can embed WebGL HTML5 content into a PDF.

Source https://stackoverflow.com/questions/65519421

QUESTION

NoClassDefFoundError: com/couchbase/client/java/error/TemporaryFailureException

Asked 2020-Aug-27 at 12:14

I am using OpenJDK 11.0.5 java version and couchbase java client version 2.6.0. It works when called through a main class but when I am hitting through my api, it throws NoClassDefFoundError. Full stack trace below :

I am just calling a method from another jar, no modifications whatsoever. The jar works well separately. I checked my code against the master branch, no changes in that.

I tried upgrading the couchbase client version to latest 3.x.x but in vain. Can anyone please suggest what I am missing?

...

ANSWER

Answered 2020-Aug-27 at 12:14

Solved it. The problem was due to multiple versions of couchbase java-client. The main application has one version and the jar has other. Made all the java-client versions consistent and it worked. I used 2.6.0 as the java-client version.

Source https://stackoverflow.com/questions/63593394

QUESTION

Datatables only returns last row on select event

Asked 2020-Aug-05 at 11:24

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ANSWER

Answered 2020-Aug-05 at 11:24

Your problem is in getTableData method.

First, you have to initialise tableData inside for, you don't have to use a global variable. --> Problem 1 in code

Second, use invalidate (i don't know is this is totally necessary) for invalidate cached data in rows and, in the end, use table.draw. --> Problem 2 in code

Source https://stackoverflow.com/questions/63260153

QUESTION

Unknown error: Error: No valid exports main found for src\main\ui\node_modules\uuid?

Asked 2020-Jul-10 at 11:22

enter image description herei reinstall npm and i have this issue:Unknown error: Error: No valid exports main found for 'D:\travail\optimus\src\main\ui\node_modules\uuid' Angular cli v 1.7.3 Node v 13.6

...

ANSWER

Answered 2020-Jul-10 at 11:22

As I know that Nodejs version v13 had some issues. Use v12.16.3 and it's working. Either use latest v14.2.0 or official LTS v12.16.3

Source https://stackoverflow.com/questions/62832881

QUESTION

Hashtable: Only saving the last element added

Asked 2020-Jul-03 at 20:34

Whenever I create multiple students, add them to the studentclass Hashtable, and try to print the hashtable(or perform any action on it) it only holds the last Student entered.

EX: Created Students: John Taylor, Timmy Turner, Optimus Prime PrintHastable: {6=Optimus Prime ,4=Optimus Prime, 2=Optimus Prime}

How can I get the hashtable to hold all entered values as opposed to just the last one?

School Class public class School{

...

ANSWER

Answered 2020-Jul-03 at 12:51

Your problem has nothing to do with HashTable.

Your Student class has two critical errors:

You made all its member static which means they exist only once - new variables are not create when you create new instance of this class. Calling new Stident will do nothing for you, you will always overwrite any previous data.
Your constructor has the assignments backwards:
Instead of storing values passed in constructor parameters in class members you do the opposite!
You store contents of class members in parameters, basically throwing all your data in to the trash bin.

You must fix both problems for your program to work!

Source https://stackoverflow.com/questions/62715664

QUESTION

Gtk/gtkmm glarea queue render doesnt work with dedicated graphics

Asked 2020-May-19 at 18:00

I started working on a github project(a logic gate simulator) with gtkmm and epoxy. I have an optimus laptop with debian buster and nvidia-bumblebee drivers installed and everything works fine except that if i start the program using optirun or primusrun, neither the glArea->queue_render, nor glArea->queue_draw function seems to work. I have to resize the window in order to rerender the glArea widget. Also sometimes when I restart the system and compile the program it wont start with bumblebee at all and outputs the following error:

311-0-no gl implementation is available

It might by something with my system, but optirun and primusrun usually works fine.

Any Idea what might be the cause of this problem?

the renderer class:

...

ANSWER

Answered 2020-May-19 at 18:00

OpenGL is poorly integrated with GTK+3, for example on OS X, you'll have this error displayed because OpenGL is simply not implemented. Maybe this is the same case for you

In addition in gtkmm-3.18 a bug (fixed since this version) displaying this error when GLArea class was derived. But this is not your case.

If that may help you I have a similar application mixing OpenGL/GTKmm in Lecrapouille/SimTaDyn I guess this will give you the same error.

Source https://stackoverflow.com/questions/61632613

QUESTION

Laravel Policy Id Obfuscation

Asked 2020-Mar-13 at 03:23

com/jenssegers/optimus id obfuscation. It works fine but in the policy it doesn't works well when I implement it.

If I remove the policy it works fine. My ProductPolicy

...

ANSWER

Answered 2019-Mar-16 at 06:43

Since you are using Route Model Binding, Laravel will search for a Product with key and will pass that model instance to show method of your controller. If you don't want this, then change show method to something like this:

Source https://stackoverflow.com/questions/55193952

QUESTION

Detect gzip encoding to manually decompress response, but 'Content-Encoding' header missing

Asked 2019-Dec-28 at 23:38

I am using net/http library in 'Go' to make an HTTP GET request. In the response, i get 12 headers. But when i run the exact same query through postman, i get 16 headers. One of those missing is 'Content-Encoding'. I understand this must be a CORS issue.

But since i have not set the header Accept-Encoding: gzip in my request, and i am still getting the gzip encoding in response, the Go transport is not automatically decompressing the response for me. So, i need to be able to manually detect the encoding and then decompress it. But, i cannot detect if the 'Content-Encoding' header is missing in the response.

Here is my code where i try to do this:

...

ANSWER

Answered 2017-May-19 at 08:21

I gave in to the stubbornness of the uber api and added another request header, req.Header.Add("Accept-Encoding", "gzip").

Now i am getting the response header "Content-Encoding": "gzip", although i am still getting an undecipherable response body, but that's beyond the scope of this question.

Source https://stackoverflow.com/questions/44064556

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install Optimus

The workflow is performed by KNIME Analytics Platform, an open-source cross-platform general-purpose workflow management system. Before you start using the workflow, you need to install KNIME itself, Python 2.7 (if it's not already installed) and a few additional modules for Python and KNIME. The installation steps are described below. If your computer is running Windows 7 or newer or macOS 10.10 or newer, you can avail express installation scripts described in the section below. Otherwise, you will need to install Optimus dependencies manually as per Regular installation section.
Go to the Releases section of this repository, download a zip archive with the latest Optimus version and unpack it to any directory on your computer. Then, follow the instruction for your OS:. Windows users: open the installer subdirectory and double-click win_installer.cmd. It should install KNIME and Python automatically. During the installation, you will be prompted to select KNIME installation directory via a graphical window. macOS Users: open your Terminal, navigate to the installer subdirectory and execute sudo bash mac_installer.sh.
Launch KNIME, click File menu and select Preferences. A Preferences dialog should appear.
In the sidebar of the dialog, expand the KNIME item and select its Python sub-item.
Click Apply.
If no error messages are shown in the dialog, Python distribution was recognized by KNIME successfully, and no further actions are needed. Otherwise, proceed with the following steps.
Click Browse... and select file - Windows users: C:\Users\<user name>\AppData\Local\OptimusAnaconda\python - macOS users: /Users/<user name>/OptimusMiniconda/bin/python
Click OK. If no errors are displayed, you can proceed to Installing and updating workflow section.
KNIME Analytics Platform 64-bit. Note, that the procedure described above should be completed only once. So, if you get a new version of the workflow in the future, all you'll have to do is just open it with KNIME. As soon as the steps above are accomplished, your environment is ready to run the workflow. Possible Python compatibility issues: If you have several Python installations in your system, please make sure that KNIME detected the correct one. To do this, go to File => Preferences, then type "python" in the filter box. You should see two items at the left-hand side of the dialog: KNIME > Python. Click at Python and check that there're no error messages appear. If there're any, press Browse... and navigate to the python executable that was called when installing modules at the 3rd step. If you followed the instructions above precisely, you can get a path to the needed python executable by executing which python in Linux/macOS terminal or where python in Windows command prompt.
Download and install Python 2.7 64-bit if you don't have installed (it can be the case on Windows). You can download it from the official Python Downloads Page.
You can check easily if the needed Python distribution is already installed by typing python -V in your command prompt. You expect to see the output line starting with "Python 2.7". The second part of the version check is determining a bit version of your python interpreter. Follow this instruction to know whether you have a 64-bit Python or not.
Windows users: Python installation directory might not be included to your Path environment variable. That's why you might get an error message upon executing python in command prompt although it's installed. To fix this, you should add <Python_installation_directory> to Path as well as <Python_installation_directory\Scripts>. By default, these directories are C:\Python27 and C:\Python27\Scripts. You can find an instruction on changing Path variable here.
If you know you have a Python distribution installed, but find steps above too complicated, just install another Python interpreter of the needed version. Multiple versions can co-exist on the same computer fine. However, remember the directory where you install it.
Install a few Python modules needed for interaction between KNIME and Python. You can do this by executing the command below in your command prompt.
Windows users: Before, you should download and install a Microsoft C++ Complier. One of those Python modules depends on it. pip install six pandas protobuf pymspec pyopenms
Others: Before, make sure you have pip package manager available on your workstation. If you don't, execute sudo easy_install pip in the terminal to install it. sudo pip install six pandas protobuf pymspec pyopenms
Download and install KNIME Analytics Platform 64-bit. Select a package according to your operating system on the official KNIME Downloads Page.
Note: If you already have KNIME installed, make sure that its version is not older than 2.12.*. The workflow hasn't been tested with older versions.
Launch KNIME and install additional extensions.
Go to File => Install KNIME Extensions.... Available software dialog should open after this.
Check the following items in the list of available extensions: * OpenMS * KNIME Python Integration * KNIME Quick Forms (legacy) * KNIME Virtual Nodes * KNIME JavaScript Views
Proceed with the installation. You'll be asked to accept the terms of GPL license at the end.
Restart KNIME after the installation is finished.

Support

Some errors can appear in the application log that interrupt workflow execution. A node caused an error will be the left-most node with a red circle in its right side. In addition, you should see error output in KNIME Console. Below, you can find solutions for some common issues.

Find more information at: