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In a systematic review, the process of screening, extracting data, and selecting relevant articles can be quite challenging and time-consuming. These steps require careful evaluation of studies to ensure the inclusion of high-quality and relevant research. Due to the complexity of this process, I am interested in learning more about free software tools that can assist in streamlining these tasks. Having access to such tools would help in managing references, organizing data, and making the review process more efficient and systematic. Could you provide details on the available free software options for conducting systematic reviews?
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or a link to any other free software or website that can be used to calculate combination index?
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C(n, k) = n! / (k!(n-k)!)
where n is the total number of items, k is the number of items to choose, and ! denotes the factorial.
Just use yhis formula
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Kindly suggest any free software for scaffold hopping?? I have a pharmacophore and need its various possible derivatives.
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For scaffold hopping, consider using GraphGMVAE, a deep learning tool for generating scaffolds efficiently. Alternatively, RDKit is an open-source cheminformatics library that supports scaffold analysis and molecular transformations.
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Do anyone know which output in Jamovi or JASP can be used to calculate RM-correlations (also known as within-subject correlations) ?
In the past I used the between-subject contrast output from RM-ANOVA in SPSS, but as non-academic, I am using free software such JASP or Jamovi. I have already read different references including:
... but the r do not match.
While accounting for between-individual variation, i also need to compute partial correlations between longitudinal data.
Anyone has any clue? Thanks in advance
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I am not sure what you are looking for, but wouldnt be a linear mixed model aka. multilevel model be an option? You are calculating a "fixed" effect, which is the effect for all participants, as well as "random" effects (intercept and slopes) for each participant. It uses partial pooling, i.e. it preserves all data, allows individual deviations from the fixed effect (the random part) and calculated individual slopes.
MLM is useful for clustered data, as well as longitudinal data. It is flexible to calculte a slope or curve for the "time" variable, but also may treat "time" as single measures / factors, like in rmANOVA. Additionally, MLM is recommended over rmANOVA, since it makes less assumptions, may handle missing data (drop out), gives better inferential estimates, and the overall results are more robust and better to generalize due to the shrinkage effect of MLM.
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Hi, can someone suggest a good free software for analyzing FCS files? I analyzed my data with the free trial of FCS Express. I need software to install on my personal computer.
Thanks
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thanks a lot David M Jameson
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Hello! I just wonder if there a free software to draw a graphical abstract where I want to draw a simple picture of a reactor and few chemical reactions
Thanks!
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This question was asked twice already but it was more thant 6y ago each, I hope there is newcomers in the software scene.
What software (as free as possible) could I use to set up a chemical compound database in our group ?
Ideally, this db would need :
- to be easily incremented regularly by students putting their new final molecules
- to be searchable by structure
- to calculate easy things as MW, TPSA, LogP (if possible)
I'm not against getting fingers inside conding but as low as possible as I'm a more chemist than a dev :)
Thanks for your answers,
François
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It depends on which kind and volume of data you will use. Do you need the chemical substructure search or it will be enough text and number search? How big (in Gigabytes) you expect will be your DB? Practically, it can be determined from the volume of your graphical data and possibility to have this data as images (.bmp; .png; .jpeg e.a.).
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I used the trial version (time limited) of this software and its time end. I will use for my educational studies. How can I find to free software licence (non commercial).
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Hi, Did you attempt to contact Dr. Friedrich Menges at info@effemm2.de? I believe you will have no trouble obtaining a license if you require it only for academic purposes (I have one myself).
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What are free software to fit XRR data for thin film structure?
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Thank you very much Prof. Gerhard Martens
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Is there any free software for caring out these calculations.
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Key Considerations
Energy Binning: Divide neutrons into energy groups for spectral analysis.
Direction: Consider the direction of neutrons for angular flux distributions.
Statistical Uncertainty: Run sufficient events to reduce statistical errors.
Example Code Snippet
cpp// In your sensitive detector class G4bool MySensitiveDetector::ProcessHits(G4Step* step, G4TouchableHistory*) { G4Track* track = step->GetTrack(); if (track->GetDefinition() == G4Neutron::NeutronDefinition()) { G4double energy = track->GetKineticEnergy(); // Increment neutron count in appropriate energy bin // Record position, direction, etc. as needed } return true; } // In your main program void AnalyzeResults() { G4double area = /* ... */; // Area of your detector surface G4double time = /* ... */; // Total simulation time G4int neutronCount = /* ... */; // Total neutrons counted G4double flux = neutronCount / (area * time); G4cout << "Neutron flux: " << flux << " n/cm^2/s" << G4endl; }
Remember to adjust the flux calculation based on your specific geometry and requirements. Geant4 provides various tools and classes to help with particle tracking and scoring, so explore the Geant4 documentation for more detailed information on available methods.
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Is there any free software available for analyzing GC data? I have some runs from a GC-2014 system with files in the .gcd format, and I'm looking for a tool to calculate peak areas and perform other analyses on my own laptop. Are there any alternatives to GCSolutions that can handle this file type?
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To analyze GC data (.gcd files) on your laptop, use OpenChrom, a free, open-source tool supporting various chromatography formats. It offers peak integration, area calculation, and other analyses. Alternatively, Chromeleon (free version), LabVIEW, or Python-based libraries like PyChrom can also be used for data processing and analysis.
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Hello, I’m looking for a free or open-source optical simulation software that could help with simulating and analyzing the performance of multilayer coatings, specifically for antireflective applications. Does anyone have recommendations or resources? Additionally, if anyone has experience with simulating multilayer structures and could provide guidance on key steps or tools to use, I’d be very grateful. Thank you in advance for your help!
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  • Because there is many software but which one is best.
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Could anyone suggested molecular dynamic analysis free software tools name and link?
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Use GROMACS for the same
For plotting graphs n analysis you can use QTgrace.
Regards
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Can you tell pros and cons of each fluorescence in situ hybridization free softwares? have you used it in impact articles?
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Fluorescence in situ hybridization (FISH) analysis software is used to process and analyze FISH images to quantify and interpret the spatial distribution of nucleic acids within cells. There are several free software options available for FISH image analysis, each with its own set of features, advantages, and limitations. Below are some of the commonly used free FISH analysis software tools along with their pros and cons:
1. ImageJ/FIJI
Pros:
Open-source and free.
Highly customizable with a vast array of plugins.
User-friendly interface for basic image processing.
Widely used in the scientific community.
Cons:
Can be complex for advanced FISH analysis without the right plugins.
Steeper learning curve for new users.
May require programming skills for extensive customization.
2. CellProfiler
Pros:
Open-source and free.
Highly flexible and can be tailored to specific FISH analysis needs.
Batch processing capabilities for high-throughput analysis.
Strong community support.
Cons:
Can be time-consuming to set up for complex analyses.
The learning curve can be steep for users not familiar with image analysis pipelines.
3. QuPath
Pros:
Open-source and free.
Designed for pathology image analysis, which can include FISH.
User-friendly interface with object classification and annotation tools.
Supports both brightfield and fluorescence imaging.
Cons:
May not be as specialized for FISH as other software.
Less commonly used for FISH analysis compared to ImageJ/FIJI or CellProfiler.
4. Icy
Pros:
Open-source and free.
Offers a variety of plugins for FISH analysis.
Interactive interface for real-time analysis.
Cons:
Less well-known and therefore has a smaller user community.
The documentation and support may be less comprehensive compared to other tools.
5. Biotools
Pros:
Free for academic use.
Specialized for FISH and other cytogenetic analyses.
User-friendly with a focus on ease of use.
Cons:
May not be as flexible or extensible as open-source software.
Limited to academic use.
As for their use in impact articles, these software tools have been used in various high-impact publications. The choice of software often depends on the specific requirements of the study, the expertise of the researchers, and the resources available.
When using these tools for research that will be published in high-impact journals, it is important to ensure that the software is fit for the purpose, that the analysis is rigorous, and that the methodology is well-documented. Peer reviewers often look for the validity and reliability of the image analysis methods used in a study.
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Critical Question:
What are the significant issues with Existing Software Engineering?
Important Note:
During this trip through the significant issues of existing software engineering issues, we will cite false claims in unlimited publications, technologies, tools, research, teaching, programs, developments, and others. We urge everyone not to take this personally. Anyone may disagree with the critical question, but please respond kindly. We experienced many bunches and losses and will speak to everyone about them later.
Motivations:
Experience as a software engineer for more than 40+ years as a practitioner and a Full academic professor, and we mastered every aspect of Software Engineering in different ways and interpretations than other claimed gurus in SWE.
Many software engineering practitioners and academics (including SJSU, where I am a full professor) present many false claims about SWE; all they see and know is the programming aspects of software engineering. Have a different understanding & knowledge of SWE, and they are missing the essential stages of SWE:
1) The Problem Space (Analysis) – Understanding the problem and representing the "WHAT."
We are talking about the functional and non-functional requirements, the responsibility, the collaboration of the classes, and the testing aspects of modeling these problem properties. Unfortunately, this Problem Space does not exist in teaching, training, research, and practice. However, the Problem Space is the most critical stage of software development in all fields of knowledge; By mastering the Problem Space, we can avoid many significant problems, including many failures.
2) The Solution Space (Design, Architecture, Coding) –Creativity of the solution and represent the "HOW-TO." This phase has many problems: 1) there are many solutions, 2) it Would lead to many different modeling techniques 3) The majority of research in SWE IS USELESS. Examples are many different modeling, architecture techniques, tools, and languages all over the solution space. Look at this statement carefully:
"if you do not understand the Problem Space, the outcome of the Solution Space is one of the following alternatives:
a) Useless Development and cancelation of the development – Billions of $s down the drain,
b) Software systems with maintenance nightmare, which causes a lot of system failures and cancelations after 5 to 6 years."
Unfortunately, in practice, coding represents 95% of the software development of any system.
We need to:
1. Unify the way we do everything in software engineering research and development
2. Emphasis on the Art, Science, and Engineering of Software Engineering
3. Stabilize the Engineering of Software
4. Standardize all aspects of Unified Software Engineering
5. Understand and accurate Execution of Software Quality
6. Allow Creativity and Innovations in Software Engineering
7. Prevent Software Maintenance
8. Unified and stabilize Methodologies, Techniques, and Processes
9. Reduce Cost and Effort
10. Produce of High Quality and Maintenance Free Software & Systems
11. Explore and Development of new Disciplines.
12. Free the Software Independency of Hardware
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Significant issues in existing software engineering include:
  1. Technical Debt: Accumulation of suboptimal code that complicates future development.
  2. Poor Requirements Management: Incomplete or changing requirements lead to project scope creep.
  3. Lack of Collaboration: Silos between teams can hinder communication and integration.
  4. Quality Assurance Challenges: Insufficient testing practices may lead to bugs and vulnerabilities.
  5. Rapid Technological Changes: Difficulty in keeping up with new tools and methodologies.
Other issues might include burnout among developers, inadequate documentation, and insufficient focus on user experience.
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I need to do energy decomposition analysis for my molecules. Is there any free software with which I can perform this job? I am using windows and not familiar with linux environment. Any suggestion is much appreciated.
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Chuck A Arize thanks a lot for your valuable suggestion
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Hello ,
I'm starting a new position and I want to use a CDF program to get some thermo-fluid dynamics in active buimding facades (or even inside).
Do you have any recommendations on what program to use?
Note that this is going to be my first experience in such programs.
Thank you in advance.
Joseph
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"Is there an alternative to ProteinWizard MS Convert for converting Synapt Waters files to a format compatible with MaxQuant, or is there any free software available that can directly process these files for protein identification?"
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Hi,
Matrix Science´s Mascot Software can do, but it´s a commercial software.
Best regards
Sebastian
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Hi
I would like to do molecular docking for my protein with metalloids such as arsenate, nitrate, selenate. I am able to dock for nitrate and selenate on the CB dock website. However, I am getting errors when I try to do that for arsenate. Is there a way to find why the error message and how to fix it in CB dock? or please suggest good and reliable free software for docking in Mac OS? I have the latest version of OS software (Monterey).
Please suggest or recommend, how to perform this work.
Thanks in advance
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Hello experts,
Does anyone know any free software about retention index prediction ?
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Several free software options for predicting gas chromatographic retention indices include
1-DeepReI:which uses deep learning for accurate predictions.
2-Mordred: an R package for molecular descriptor calculations.
3-ChemmineR: can also be adapted for retention index predictions through machine learning.
4-ACD/Labs offers trial versions of their software for users seeking advanced features.
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Hi.Could anyone suggest a few free software which is easy to use to conduct the transitivity of a text in a novel ?Thank you !
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لحد الساعة ليس لدينا فكرة عن أي برمجيات اصطناعية بإمكانها تحميل النص الروائي وتحليله، نتمنى إفادتنا برابط تحميله إذا كان متوفرا.
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A free software (web version)of blackbody radiation law is used through URL(http://39.105.188.151:3000/index)
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The blackbody radiation law plays a crucial role in the fields of physics, thermodynamics, optics, and remote sensing. However, its abstract nature and complex formulas make understanding challenging, and the difficulty in meeting experimental conditions becomes a problem in teaching. Based on the theoretical analysis of the twenty-seven expressions of blackbody emissivity, radiance, and energy density, as well as the six forms of Wien's displacement law and nine formulas for blackbody radiation peak intensity, we developed the shared online version of the Blackbody Radiation Expert (BRE,http://39.105.188.151:3000/index) software for practical teaching and research. This free software provides theoretical and practical experience for teaching blackbody radiation, enriches teaching resources, and offers valuable insights for the reform and optimization of similar courses.BRE can used for analysis of remote sensing field.
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To do life cycle impact assessment related with asphalt/asphalt production suggest me suitable software and databases please
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I don't believe GaBI is available for free. However, they may share a demo version of the software for educational purposes. When it comes to pavement, some state DOTs have very comprehensive LCIA and EPDs which is a very a good place to start. With the upcoming FHWA low-carbon transportation materials grant we'll hopefully be seeing significant improvement in the quality of pavement LCIA and EPDs.
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TL;DR
--
I firmly believe in the free software and free science philosophy as an enabler for a real free society. As a consequence, I'm against any form of data and freedom control, intellectual property, surveillance and privacy violations, and so on and so forth.
But more than anything, I'm a supporter of that sense of "feeling at home" that you could feel in the early internet (just remind IRC, or the first websites of the early 2000's), which today has almost completely vanished.
With that in mind, I have spent the last two months creating a kind of unusual website. It is basically a personal website that I use for promotional reasons as I progress in my PhD researches. But not only that, the site has been built to be also a sort of community for scholars and people that seriously cares about freedom in computing, science, and society.
I have written an article to better explicate this concept, and I would be very happy if some of you could take a look at it. Here is the canonical URL to the article: https://www.dmi.unict.it/nfarceri/articles/welcome.eng.html.
As you noticed, it is a plain HTML text file. However, at the bottom of the article you can find a link to connect to the main site, which you can click on so as to be redirected to and thus opening the article on the main site.
Thank you all in any case for reading. Looking forward to seeing you there :-)
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Made some meaningful improvements to the site.
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I am trying to simulate a new solar cell which has almost 15 layers. But SCAPS has only 7 layers.
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1. **Inkscape**: Inkscape is a free and open-source vector graphics editor that can be used for creating and manipulating multi-layered designs. It supports up to 999 layers, making it suitable for your requirement.
2. **GIMP (GNU Image Manipulation Program)**: GIMP is a free and open-source image editing software that can handle multi-layered images. It supports up to 256 layers, which should be sufficient for your needs.
3. **Krita**: Krita is a free and open-source digital painting and illustration software that offers a powerful layering system. It supports up to 100 layers, which is more than enough for your simulation.
4. **Paint.NET**: Paint.NET is a free image and photo editing software that provides a user-friendly interface and supports multiple layers. It can handle up to 99 layers in a single image.
5. **Photoshop (trial version)**: While Photoshop is a paid software, it does offer a free trial version that you can use to test its layering capabilities. The trial version supports up to 999 layers, which should meet your requirements.
6. **Affinity Photo**: Affinity Photo is a professional-grade image editing software that offers a free trial version. It supports up to 16,777,216 layers, far exceeding your need for 15 layers.
Partial credit AI
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Please, can the fragmentation obtained from the mass spectrometry be predicted more easily using any free software? Kindly recommend it, thanks.
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Hi!
What are you planning to fragment with MALDI-TOF and would you like to predict the fragmentation of: peptides, proteins, glycans, fatty acids, oligonucleotides, ...?
BTW, it's mass spectrometry, not spectroscopy :)
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I like PCW and profex as they are free softwares. It would be great to put the cif, and str files together with my samples to better identify. I work with XRD applied to mineralogy.
Thanks!
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Hello. It is not a problem. All these files are in text format and can be edited, for example, in a notepad. cif files contain all the necessary data for the PowderCell cel file.
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My thesis is on "effects of CNT on warm mix asphalt," but i couldn't get the CNT and i am running out of time. So i want to run a simulation test but the software that can do that is the problem.
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I think you can run such simulation on LAMMPS. It's an open source, you just have to provide input files.
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Thanks in advance!
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I have sent my method to your email, hoping it will be helpful to you.
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I have synthesized an organic compound. However, I do not have the access to scifinder or reaxys. I would like to know whether the molecule I have prepared is new or already reported. Is there a free software where I can draw the structure of the compound and it can give me some information about it?
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I want to simulate LSPR absorption peak versus wavelength spectra for distributed Ag nanoparticles on a substrate. I wish to play with the refractive index(both real and imaginery part) of the substrate and see the effect on LSPR peak intensity and peak wavelength. I have SEM images of Ag nanomorphology. So, I have prior knowledge of shape and size distribution and interparticle distances.
I guess, this kind of simulation may be possible in FDTD or Comsol multiphysics software. Somehow I feel these softwares must be too heavy and difficult to learn directly as a beginner. Instead, I am looking for any lite free software (preferrably windows based) for such simulations. Any help will be much appreciated.
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I think it will be possible by CST. CST Software is easier comparing to LUMERICAL and COMSOL.
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I know SoundPLAN and ODEON, but I want to know any free software. Thank you.
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Hi, we made a review of commercial software tools for facade acoustics some years ago. Some of them are free and might suit your needs.
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We are mounting the STRs technique on an applied 3500 device (Applied Biosystems), which we usually use only for human identification (HiD).
It turns out that we realize that reading STRs requires a different version of the Genemapper software, and that version is excessively expensive.
Does anyone know of any free software in which we can read the STR file?
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Hallo. There is no freeware for this. There used to be a software PeakScanner but its version 2 supposed to be compatible with fsa data from ABI3500/xl has many bugs, never really worked and you cannot download it from the ThermoFisher website anymore.
However, I may have a solution for you but need more information. Please contact me directly at richard.nadvornik@seqme.eu in case your request lasts. All the best Richard Nadvornik
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Hello everyone
1. Please suggest a robust free software to analysis the XRD results to obtain the corresponding 3d structure of a protein.
2. Is the xrd diffractogram with only a single peak better than a diffractogram with multiple peaks or vice versa? And what are the reasons?
3. What does raw.file show after xrd analysis?
Thanks to all
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Xpert High score software
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I have data consisting of two trends over time.
For example, the GDP and net immigration figures of the UK, from 1950-2020 (not the real data).
I can plot the 2 trend lines on the same graph and visually examine if they look like they correlate over time. However, is there any way to examine if they statistically correlate over time?
Note, this need to be a simple analysis that one can do in MS excel of other free software (e.g. JASP), as it is for a student.
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Yes, the same meaning: "rolling the window" = like = sliding the window.
Good luck Joseph Whittaker.
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Actually I want to perform RNA seq analysis via NGS platform to identify the genomic variability and diversity in specific viral strains
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Hello,
You can try out Galaxy
Regards
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Dear all,
Greetings !!
Can anyone share the list of the best software that can be used for drawing result graphs?
You can give suggestions for Paid as well as Free Software.
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So, a few days ago I had installed the free software BIOVIA Discovery Studio Visualizer to analyse certain protein ligand interactions. I observed that the pdb files which were created in my earlier work as well as the recent ones automatically got saved in the BIOVIA Discovery File Type and I can't open the files through LigPlot+. Even when I have uninstalled the entire Discovery Studio Visualiser, the file types are not changing. Can anyone guide me resolving the issue. This is the first time I have encountered something like this.
All help will be much appreciated. Thanks.
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Right click on the PDB file and navigate to open with. A list of Apps will come up and you will see "choose another App". Click on it and choose the App of your choice. You can use the option "Always use this App to open PDB files". I chose notepad and that was how I was able to convert all my pdb files to readable format using notepad.
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I want to do HRM analysis from melt curve data which was generated from RT-PCR instrument of Bio-Rad CFX96. In our lab, we have no original software from Bio-Rad (Precision Melt Analysis Software). Now, we are stuck. Any suggestion for free software that could process Bio-Rad melt curve data for HRM analysis?
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Yes, there are several free software options available for processing Bio-Rad melt curve data for High-Resolution Melting (HRM) analysis. One such option is R-based software called "HRM," which is specifically designed for HRM curve analysis. It offers various functionalities for analyzing and visualizing melt curve data, including normalization, curve fitting, and genotype calling. Additionally, "MeltDoctor" software provided by Thermo Fisher Scientific is another free tool widely used for HRM analysis. It allows users to analyze and interpret melt curve data generated by Bio-Rad instruments. Both of these software options offer user-friendly interfaces and comprehensive tools for researchers conducting HRM analysis. Researchers can choose the software that best fits their specific needs and preferences while also considering compatibility with their laboratory equipment and workflows. Overall, these free software options provide valuable resources for processing Bio-Rad melt curve data, enabling researchers to efficiently analyze their HRM experiments without incurring additional costs.
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  • What are the key steps involved in designing KASP markers, particularly for genotyping purposes? Additionally, could you recommend any reliable free software tools for designing PCR primers that are compatible with KASP technology?
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Designing KASP (Kompetitive Allele-Specific PCR) markers for genotyping involves several key steps. First, identify the target SNP (Single Nucleotide Polymorphism) for genotyping. Then, design allele-specific primers that specifically amplify each allele.
These primers should have a competitive element, typically a tail or a universal tag, to allow discrimination between alleles during the competitive PCR step. Validate primer specificity and efficiency using appropriate controls. Finally, optimize PCR conditions for genotyping accuracy and reproducibility.
For designing PCR primers compatible with KASP technology, several software tools are available. KASP Designer by LGC Biosearch is a widely used and reliable tool for designing KASP assays.
It helps design allele-specific primers and provides information on potential amplicon size and SNP position. Another option is Primer3, a versatile primer design tool that can be configured for KASP primer design by specifying parameters such as allele specificity and competitive tails. Both tools are accessible online and can assist in the efficient design of KASP markers for genotyping purposes.
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Is there any free software which is helpful to do dispersion modelling of the pollutants emitted from the line sources like vehicular source and also suitable for hilly region?
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try getting them from USEPA website
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I want to free download software available to assess soil moisture budget using the Throtnwaite and Mather method
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refer to the original publications or reliable sources for the equations and methodology associated with Thornthwaite and Mather Soil Moisture Budget calculations.
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Hello everyone! I'm Martin Pavarotti from Argentina. I'm in search of a free version of the VOLOCITY software for Mac. Could anyone help me with this?
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Volocity 3D Image Analysis Software is the only solution that provides all the tools you need to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems and is fully integrated for a seamless user experience. Make discoveries and answer complex questions that you could not before. Visualize samples in 3D so they can be viewed from any direction for a more complete picture. Greatly improve your image and data quality with powerful restoration. Measure shapes, volumes and distances with precision. Relate cellular structure to function, and identify trends for a greater understanding.
Regards,
Shafagat
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I am interested in the analysis of extracellular electrophysiological recordings and specifically I would like to know if there is any free software that contains modules for Multi Unit Analysis, artifact removal and Denoising, etc. and that could accept data in .txt format.
Thank you so much for your help.
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Regarding spike sorting, you may also have a look at spike interface :
It tries to make a bridge between most of the current methods or softwares in spike sorting.
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gallery API50CH
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You can use API 50 CH gallery is the "APIweb" software provided by bioMérieux. It is specifically designed for the interpretation of API strip results and allows for the identification of a wide range of bacterial species.
APIweb is a web-based application that can be accessed through any internet browser. It provides a user-friendly interface where you can input the results obtained from the API 50 CH gallery and obtain the corresponding bacterial identification. The software also provides additional information about the identified species, including their characteristics and relevant literature references.
To use APIweb, you will need to create an account on the bioMérieux website and follow the instructions provided to access the software. It's important to note that while the software itself is free, you may need to purchase the API 50 CH strips separately.
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Can anyone please introduce me a free software for measuring light and electron microscope when taking a photo (for light and electron microscope photos, as well as when working microscope) diameter, perimeter, and area in the form of Circular, polygon, and filamentous or tubular forms in terms of width and length?
What about color changes?
Thank you in advance,
Jafar sabouri
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Dear Christopher,
thanks a lot for your kindness,
jafar
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I'm having trouble finding software to do this. I downloaded the Kubios Standard, but it looks like it's only for humans. Kubios Scientific does the analysis I need, but I'm from Brazil and for me the price is expensive, so I'm trying to find a free software.
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Hello Gabriel,
Our research group has an open-source python package https://github.com/scientisst/BioSPPy
that is designed for biosignal processing. Though we have only use it in humans, I think you could try for rats, since it is very easy to adapt.
At the moment we are adding the HRV analysis module.
Though it is still not the same as kubios, we could sure use your help to understand which features should be added to the module.
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For the measurement of particle size from XRD TEM SEM etc
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For measuring particle size, there are several free software options available, each with its own set of features and capabilities. Here are a few you might consider:
ImageJ: A popular open-source image processing program developed by the National Institutes of Health. It's widely used for analyzing particle sizes in images, especially in scientific research. ImageJ supports various image formats and provides tools for measuring and analyzing particle size distributions.
Gwyddion: This is a modular program for scanning probe microscopy data analysis but can also be used for analyzing particle sizes. It's open-source and provides a range of tools for data visualization and processing.
Scikit-Image: A collection of algorithms for image processing in Python. While primarily a library for Python, it's suitable for those comfortable with scripting and programming. It's useful for more complex or customized particle size analysis tasks.
Fiji: An extension of ImageJ, Fiji is “batteries-included” - meaning it has many plugins pre-installed for various image analysis tasks, including particle size analysis.
OpenCV: This is more of a computer vision library, but it can be used for particle size analysis if you have programming skills, particularly in Python, C++, or Java.
Each of these tools has its own learning curve and may require some background knowledge in image processing or programming. The choice of software often depends on the specific requirements of your analysis, the complexity of the images, and your comfort with programming or using specialized software tools.
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Hi friends,
I am just wondering about the free/ paid software researchers are using for demonstrating their lengthy conceptual models or frameworks. I am doing a lot of literature reviews and desperately looking for any platforms where i can easily create my frameworks. Creating too many tables and arrows on word makes my life hell.
Any help / suggestions in this regard is highly appreciated.
Thanks
Surej John
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Here are a few popular ones:
1. Lucidchart: Lucidchart is a web-based diagramming tool that offers a free version with limited features. It provides a wide range of shapes, symbols, and templates that can be used to create conceptual frameworks and other types of diagrams. Lucidchart also supports collaboration, allowing multiple users to work on diagrams simultaneously.
2. draw.io: draw.io is an open-source diagramming software that can be used to create conceptual frameworks. It offers a user-friendly interface with various shapes and connectors to design diagrams. draw.io can be used as a web application or downloaded as a desktop application for offline use.
3. Coggle: Coggle is an online mind-mapping and brainstorming tool that can be used to create conceptual frameworks. It allows you to create interconnected nodes and organize your ideas visually. Coggle offers a free version with basic features, and it also supports real-time collaboration.
4. Canva: Canva is a versatile graphic design tool that can be used to create conceptual frameworks and other visual materials. It provides a wide range of templates, shapes, icons, and fonts to design professional-looking diagrams. Canva offers a free plan with many features, and it also has a collaborative feature for team projects.
5. FreeMind: FreeMind is a free and open-source mind-mapping software that can be used to create conceptual frameworks. It offers a simple and intuitive interface for organizing thoughts and ideas visually. FreeMind supports various features like node customization, hyperlinks, and export options.
6. yEd Graph Editor: yEd Graph Editor is a powerful desktop application for creating diagrams, including conceptual frameworks. It provides a wide range of layout algorithms and customization options to create visually appealing diagrams. yEd Graph Editor is available for free and supports various operating systems.
Hope it helps
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Dear Colleagues,
Is there any free software for GPS Vehicle Tracking?
Regards
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There are several free and open-source GPS vehicle tracking solutions available. Here are a few options you can consider:
1. **Traccar**:
- Traccar is an open-source GPS tracking platform that supports various GPS tracking devices and protocols. It provides both web and mobile interfaces for tracking and managing devices.
2. **OpenGTS**:
- OpenGTS (Open GPS Tracking System) is a full-featured web-based GPS tracking system that provides a rich set of features for tracking vehicles or other assets.
3. **GPSWOX**:
- While GPSWOX does offer paid plans, they also have a free plan with limited features that can be suitable for small-scale tracking needs.
4. **OwnTracks**:
- OwnTracks is more focused on personal location tracking, but it can be adapted for vehicle tracking as well. It's open-source and provides mobile apps for Android and iOS.
5. **GpsGate**:
- GpsGate offers a free version with limited features, but it can be used for basic vehicle tracking needs. They also provide a paid version with more advanced features.
Remember that while these solutions offer free versions, they may have limitations in terms of the number of devices, features, or usage. If you have specific requirements or need advanced features, you might want to consider paid solutions or explore their premium plans.
Always review the terms and conditions, privacy policies, and licensing agreements of any software you choose to ensure they meet your needs and comply with any legal or regulatory requirements in your jurisdiction.
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There's G-Fourier for Linux and MacOS. I can't make it work for Windows however. Is there some Fourier analysis software that would allow me to make 2D and 3D electron density maps on a Windows machine?
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Yes, there are free software programs available for Windows machines that can be used to generate electron density maps, typically for use in the field of computational chemistry and crystallography. Here are a few options:
PyMOL: PyMOL is a widely used molecular visualization tool that can generate electron density maps. While the free version of PyMOL has limited functionality, it can still be used for basic electron density map visualization. You can download the open-source version known as "PyMOL2" for free.
Avogadro: Avogadro is an open-source molecular editor and visualization tool that can also generate electron density maps. It is designed for general chemistry, and it's user-friendly.
Jmol: Jmol is another open-source molecular visualization program that can be used to visualize electron density maps. It's not as feature-rich as some other tools, but it's free and relatively easy to use.
XCrySDen: While primarily a crystallography visualization tool, XCrySDen can also generate electron density maps. It's open source and supports a variety of file formats.
Vesta: Vesta is a visualization program for structural models, and it can display electron density maps generated from crystallographic data. It's free and widely used in the crystallography community.
Remember that the availability and features of these software programs may change over time, so it's a good idea to visit their official websites for the latest information and downloads. Additionally, the quality and accuracy of electron density maps may depend on the underlying computational methods and data used, so it's essential to ensure that you have appropriate input data and settings for your specific research needs.
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I'm trying to start modeling asphaltene precipitation. Since I read studies related to asphaltene precipitation, I have found that modeling with PC-SAFT equation of state is most appropriate.
However, I don't have any software or MATLAB code that can model VLE and LLE for the system with multicomponents.
Would you please recommend me some free software or code for PC-SAFT EOS?
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Clapeyron.jl has implementation of PC-SAFT (and many other EoS) in Julia programming language.
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I have a CT scan of a human skull. I´ve edited, performing a maxillary orthognathic surgery (Le Fort I), and added two plates with 4 screws each. I´ve export this set as a whole and separated with each item in .STL.
When I add this set to any FEM software, the files do not open. In fact they open but no image appears and I cant get to manipulate, edit, do nothing with these files.
Anyone knows what am I doing wrong? Do I have to solidify? I´m using FreeCAD, Blender and mainly Meshmixer.
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I used SpaceClaim from ANSYS to detect errors and correct them.
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Hello,
I know that profex, Mercury and MAUD can all fit powder XRD data to structual data given by an CIF file for example.
However, I can't find a free software where I can fit only the peaks along a given direction, for instance only along [001]. Whenever I load my CIF file into the software it shows all possible XRD peaks you would get when you do powder diffraction, this I can obviously not fit with my thin film data.
Thank you and have a nice day,
Simon
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In GSAS-II, in Phases, select the phase you want, go to the Data tab, at the bottom, there is the option to model a preferred orientation with March-Dollase for a crystal plane. It starts with 1, to increase preferred orientation, make it lower.
However, it looks like it could have more than one plane with preferred orientation, I don't know if this is possible and I've never dealt with this, but there are peaks of the phases that completely dissappear.
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I want to draw some patient pedigrees for a manuscript. Any suggestion for free software?
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Sarvananda Letchuman- Thank you so much for the valuable answer!
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Hi,
I am working on analysis of a study where I need PSM matching . Kindly suggest a free software for PSM analysis. TIA.
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This is the paragraph from the CRAN Task View for Causal Inference on matching packages. So lots of free packages written in S/R.
  • "Matching methods are implemented in MatchIt, which provides wrappers for a number of popular methods including propensity score matching and subclassification, (coarsened) exact matching, full matching, and cardinality matching; more specialized matching methods are implemented in some of the packages below, some of which MatchIt depends on. MatchThem provides a wrapper for MatchIt with multiply-imputed data. Matching performs nearest neighbor and genetic matching and implements Abadie and Imbens-style matching imputation estimators. optmatch performs optimal matching using network flows; several other packages rely on the same infrastructure, including DiPs (near-fine matching with directional penalties), matchMulti (optimal matching for clustered data), rcbalance and rcbsubset (optimal matching for refined balance), approxmatch (near-optimal matching for multi-category treatments), and match2C (optimal matching using two criteria). Other packages include cem (coarsened exact matching), designmatch (optimization-based matching using mixed integer programming), stratamatch (matching and stratification in large datasets), FLAME (almost-matching-exactly via learned weighted Hamming distance), PanelMatch (matching with time-series cross-sectional data), and CausalGPS (generalized propensity score matching for continuous treatments)."
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I am trying to build random parameters model with heterogeneity in mean and variance (RPNB-HMV) models for road traffic crashes on a highway in India.
Random parameter Negative Binomial models are the most popular models for assessing unobserved heterogeneity in crash prediction models.
I want to know some free or open-source software like R for fitting such models.
E.g. A sample syntax of the RPNB-HMV model in R software.
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R is one popular free software for building random parameters models for count data with heterogeneity in mean and variance. R is a powerful programming language and software environment for statistical computing and graphics. It has a vast collection of packages specifically designed for various statistical modeling tasks, including count data analysis.
R packages that you can use to build random parameters models for count data:
1. lme4: The lme4 package provides functions for fitting linear mixed-effects models, including models with random parameters. It uses a maximum likelihood estimation approach and supports various model specifications and random effects structures. You can use this package to build random parameters models for count data with heterogeneity in mean and variance.
2. GLMMadaptive: The GLMMadaptive package is specifically designed for fitting generalized linear mixed models (GLMMs) with adaptive Gaussian quadrature for efficient estimation. It supports various distributions, including Poisson and negative binomial, which are commonly used for count data. GLMMadaptive allows for modeling heterogeneity in mean and variance, making it suitable for building random parameters models.
3. brms: The brms package provides a flexible interface to fit Bayesian multilevel models using a syntax similar to lme4. It utilizes Stan, a powerful probabilistic programming language, for Bayesian inference. brms allows for specifying complex models with random effects and supports a wide range of count distributions, including zero-inflated and hurdle models.
4. MCMCglmm: The MCMCglmm package is focused on fitting multilevel models using Markov chain Monte Carlo (MCMC) methods. It provides a Bayesian framework for estimating random parameters models with different variance components. While it doesn't have built-in support for count data distributions, you can use transformations or link functions to model count outcomes.
These packages offer different approaches and functionalities for building random parameters models for count data in R. They provide flexibility, extensive documentation, and user communities for support. You can install these packages in R using the `install.packages()` function and access their documentation and examples through the R help system.
Good luck
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Please suggest me a free software to make conceptual and theoretical frameworks
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Various free software tools for diagramming or mind-mapping capabilities are:
1. draw.io: draw.io is a free, web-based diagramming tool that allows you to create various types of diagrams, including conceptual frameworks. It provides a user-friendly interface with a wide range of symbols and shapes to construct your framework. It also offers collaboration features and the ability to save your diagrams locally or in cloud storage services.
2. Lucidchart: Lucidchart is an online diagramming tool that offers a free version with limited features. It provides an intuitive interface and a variety of shapes, templates, and icons to create conceptual frameworks. Lucidchart allows you to collaborate with others, export your diagrams, and integrate with popular tools like Google Drive and Slack.
3. Coggle: Coggle is a web-based mind-mapping tool that allows you to create visual representations of your conceptual and theoretical frameworks. It offers a simple and intuitive interface with drag-and-drop functionality. You can collaborate with others in real-time and export your mind maps as PDF or image files.
4. MindMup: MindMup is a free online mind-mapping software that enables you to create hierarchical structures and relationships between concepts. It offers an easy-to-use interface, real-time collaboration, and the ability to import or export mind maps in various formats. MindMup also integrates with cloud storage services like Google Drive and Dropbox.
5. XMind: XMind is a popular open-source mind-mapping software that provides a free version with basic features. It offers a range of templates, styles, and customization options to create conceptual frameworks. XMind allows you to export your mind maps in various formats, including PDF, image files, and Microsoft Office formats.
These are starting point for creating conceptual and theoretical frameworks, and each has its own unique features and interface. You can explore them and choose the one that best suits your needs and preferences.
Good luck
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In my study i am using nanocellulose based membrane for the adsorption study of dye and heavy metals
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Crack version of orijin lab 2019 b should be a prominent one by which you can easily analysis your obtained experimental data also it will helpful for the mathmatical modelling.
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Free software to gather a tremendous amount of research material.
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When building a literature review, researchers often use a combination of software tools and online platforms to gather and manage their research sources efficiently. Here are some popular software tools commonly used for this purpose:
  1. Reference Management Software: Reference management software helps researchers organize and manage their bibliographic references and citations. These tools are useful for keeping track of research papers, books, and other sources that are relevant to the literature review. Some popular reference management software options include:Zotero: A free and open-source reference manager that allows users to save, organize, and cite sources. It integrates well with web browsers and word processors. Mendeley: A reference manager and academic social network that enables users to organize their research library, collaborate with others, and discover new research. EndNote: A comprehensive reference management tool with advanced features for organizing and citing references. It is widely used in academic and research settings.
  2. Search Engines and Databases: To find relevant research papers and articles for the literature review, researchers use various academic search engines and databases. Some popular ones include:Google Scholar: A free search engine that indexes scholarly literature across various disciplines. PubMed: A database primarily focused on life sciences and biomedical research. IEEE Xplore: A digital library for research articles, conference papers, and standards in engineering and computer science. ScienceDirect: A platform that provides access to scientific, technical, and medical research articles and journals.
  3. Online Libraries and Digital Repositories: Many universities and research institutions have their online libraries and repositories where researchers can access academic publications. Examples include institutional websites, university libraries, and open-access repositories like arXiv and SSRN.
  4. Collaboration and Note-Taking Tools: Collaboration tools and note-taking software can be helpful for researchers working in teams or those who need to organize their thoughts and ideas efficiently. Some commonly used tools include:Microsoft OneNote: A note-taking application that allows users to create notebooks and organize information using text, images, and multimedia. Evernote: A cross-platform note-taking app that allows users to capture ideas, web pages, and documents and sync them across devices. Google Docs: A cloud-based word processor that facilitates collaboration and real-time editing with multiple users.
Remember that the choice of software will depend on individual preferences, the specific requirements of the literature review project, and any institutional or collaborative considerations
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Dear network. I'm looking for free friendly software for structural equation modeling. I already used Lisrel free version. But also download GSCA PRO for generalized structural equation modeling. How did gsca pro come out? Do you know other free software for the MES? thank you so much.
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Thank you so much
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For example, I want to capture on Facebook all pages or accounts three months ago communicated a particular event, say an Earthquake.
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Thanks a lot. Your response provides useful insights into where I can start.
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For Material Modelling apart from Material studio are there any open source free softwares available for researchers?
Material studio unfortunately is not free anymore, already using MATLAB and Simulink but I am looking for products similar to Material studio, any advice will be greatly appreciated.
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Indeed there are so many different tools that your best option is to be more specific about what you want to do. Essentially, your question is comparable to “I want to drive, which car should I choose?” I can answer, “I really like Ferraris” but it could be the inappropriate car to go rallying in the mountains.
Many of the suggested codes posses a large set of capabilities. Some of them excel in particular cases (for instance, periodic vs non-periodic materials), some offer classical approaches, others quantum mechanical. Exploring them all requires a quite large amount of time. And you might still miss the tool best suited for your task.
Therefore, my suggestion would be that you try to be more specific on your needs. And the answer might be narrower but more to the point.
Regards,
Roberto
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I am looking for good and preferably free software that will visualize a set of x, y, and z coordinates. I haven't had much luck with ImageJ or MATLAB. Specifically, I am trying to visualize 3D single-molecule localization microscopy data points. Any suggestions are greatly appreciated!
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  1. Tableau: Tableau is a widely used data visualization software that offers 3D capabilities. It allows you to create interactive visualizations and dashboards using various data sources. While Tableau primarily focuses on 2D visualizations, it does provide limited 3D visualization options.
  2. D3.js: D3.js (Data-Driven Documents) is a powerful JavaScript library for creating interactive data visualizations on the web. Although primarily known for 2D visualizations, D3.js does support 3D visualizations using libraries like Three.js, allowing you to create interactive and dynamic 3D visualizations directly in the browser.
  3. ParaView: ParaView is an open-source data analysis and visualization tool specifically designed for large-scale scientific data. It supports 3D visualization of complex datasets, including scientific simulations and computational models. ParaView offers advanced features such as volume rendering, isosurfacing, and interactive exploration of 3D data.
  4. MATLAB: MATLAB is a widely used software environment for numerical computing and data analysis. It provides built-in functions and toolboxes for 3D visualization, allowing you to create interactive plots, surface plots, volumetric visualizations, and more. MATLAB's powerful graphics capabilities make it suitable for scientific and engineering applications.
  5. Unity: Unity is a popular game development engine that can also be utilized for 3D data visualization. It offers a wide range of tools, visual scripting, and 3D rendering capabilities to create interactive and immersive visualizations. Unity is particularly useful when you want to create interactive simulations or virtual reality experiences based on your 3D data.
  6. Blender: Blender is a versatile open-source 3D modeling and animation software. While it is primarily used for creating 3D models and animations, Blender also provides visualization features that allow you to import and display 3D data in various formats. It offers a comprehensive set of tools for rendering, lighting, and shading to create visually appealing 3D visualizations.
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For solving chemical parameters of a single crystal, which softwares are helpful, in addition to that, which is good for doing docking analysis
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Contact Schrondinger and request for free trial version. The whole package is just awesome and covers many computational parameters.
If you have linux system, then you will also be able to perform MD simulation in the same package. Good luck!
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i want to do a research that using a modified Stroop task.
is there any free software that i could use, where I could change the words used in the task?
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Yes, there are several free software options available that you can use to modify the words used in a Stroop task or create your own custom Stroop task. Here are a few popular choices:
1. PsychoPy: PsychoPy (https://www.psychopy.org/) is a free and open-source software for creating experiments in psychology and neuroscience. It offers a user-friendly graphical interface where you can design and customize your Stroop task. PsychoPy allows you to easily change the words, colors, and other parameters of the task.
2. OpenSesame: OpenSesame (https://osdoc.cogsci.nl/) is another open-source experiment builder that allows you to create and modify Stroop tasks. It provides a drag-and-drop interface and a scripting language for more advanced customization. OpenSesame is highly flexible and suitable for various experimental designs.
3. E-Prime: E-Prime (https://pstnet.com/products/e-prime/) is a widely used commercial software for designing and running psychological experiments. Although the full version of E-Prime is not free, you can download a free trial version with limited functionality. E-Prime offers a visual interface and a scripting language for customizing Stroop tasks.
4. Inquisit: Inquisit (https://www.millisecond.com/products/inquisit/) is another commercial software used for creating and running psychological experiments. It has a user-friendly interface and supports customizing Stroop tasks. Inquisit also provides scripting capabilities for advanced customization.
These software options offer various features, flexibility, and support for creating customized Stroop tasks. Depending on your specific needs and preferences, you can choose the one that suits you best. It's advisable to visit their respective websites to explore the features, documentation, and tutorials provided by each software to assist you in creating and modifying your Stroop task.
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Hi, I would like to know if there are free software for implementing non parametric testing, ki2 and CHAID, log regression, PCA and similar tasks.
I use JASP but I would like to learn a new software with additional tests
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R
.
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I heard about CANOCO but it isn´t free. 
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Hi everyone, any suggestion for free software for overlaying a DFT structure to an X-ray structure, please?
Thank you
Musa
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It seems like you are trying to compare a DFT optimized structure with the crystal structure. I think 'ORTEP' should work for the same.
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Hi,
I am currently screening more than 2000 compounds virtually on Vina, but I would like to perform covalent docking. Unfortunately, Vina's functionality is limited as its requires manual designation of the reactive atoms on the ligands. Is there any alternative that is free for academic purposes and suited for this sort of task?
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hi my friend
I used AutoDock 4.2 software for covalent docking. also, u can use moe software.
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Do you know any alternative free software to draw flow diagrams?
Thank you in advance!
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You can use draw.io
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I am looking for free software work on the ocean optics spectrometer. I bough used one without software 2000+
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Dear prof. Abdulkhaleq Alwahib
I hope you be fine.
Please send an e-mail for me by subject "ocean optic".
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I need to perform DEM simulation for particle packing of CDW-based aggregates (geopolymer mortars), Can you folks recommend a free software, student version, trial version or code-based simulation that has some worked examples?
Thanks for your time and help.
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YADE is open source and free to use for anyone. https://yade-dem.org/doc/ Very easily installed on most Linux distributions.
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I intend to know the list of software that can be used in simulating the Electrochemical properties of novel electrode or electrolyte materials for both battery and supercapacitors.
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Hello Prof Ajit Singh, Thank you so much for the answers you provided. I really appreciate!
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I need to calculate theoretical CD-spectra of a few organic compounds. I never dealt with CD-spectroscopy nor I have any experience with theorethial calculations. Still I hope that there is a software designed to solve this issue.
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Thanks
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Monte Carlo
free software
cad design
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My Msc student is doing a project which involves geochemical analysis of sedimentary rocks which may be of volcanic origin. She needs to plot the data on different discriminative diagrams. Does anybody know of any good, free software for this purpose.
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Albeit indeed originally designed for igneous and metamorphic rocks, GCDkit would plot anything. I often show my students an example of plotting a sample dataset on religion in Switzerland. This system also allows, relatively easily, adding new plugins and user-defined plot templates. See blog.gcdkit.org.
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Hi, I am doing my dissertation as a systematic review and meta-analysis on the efficacy of daratumumab in relapsed and refractory multiple myeloma. I am using clinical trials as my source and do not know how to conduct a meta-analysis on it as there are no control groups. My goal is to create a forest plot and gain an overall response ratio (95% CI) and generate a p-value. I would ideally like to do this on RevMan or any other free software as I do not have access to any of the paid software.
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Meta-analysis is a statistical method that combines results from multiple studies to generate a summary estimate of the effect size of a particular intervention or exposure. The steps to conducting a meta-analysis for clinical data include:
  1. Define the research question and identify relevant studies: Determine the clinical question or problem that the meta-analysis will address, and identify studies that are relevant to the question. This can be done by conducting a comprehensive literature search using databases such as PubMed, Cochrane Library, and Embase.
  2. Evaluate the quality of the studies: Assess the quality of the studies using established criteria, such as the Cochrane Risk of Bias Tool or the Newcastle-Ottawa Scale. This will help to determine which studies are of high enough quality to be included in the meta-analysis.
  3. Extract data from the studies: Collect relevant data from each study, including information about the study design, sample size, intervention or exposure, outcome measures, and effect sizes.
  4. Analyze the data: Use statistical software such as R or STATA to analyze the data. Depending on the type of data and research question, the analysis may involve calculating summary statistics, conducting regression analyses, or using other statistical methods.
  5. Conduct a meta-analysis: Combine the results of the individual studies to generate an overall estimate of the effect size using statistical methods such as fixed-effect or random-effects models.
  6. Interpret the results: Interpret the results of the meta-analysis and draw conclusions about the effectiveness of the intervention or exposure. Assess the level of heterogeneity between studies, and conduct sensitivity analyses to explore the robustness of the results.
  7. Report the findings: Write up the results of the meta-analysis in a clear and concise manner, including details about the studies included, the methods used, and the results of the analysis. This should be done following established reporting guidelines such as the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement.
It's important to note that conducting a meta-analysis requires a solid understanding of statistical methods and research design, so it's recommended to seek the help of a statistician or experienced researcher to ensure the analysis is conducted appropriately.
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Good afternoon,
I previously used a free software called Angioquant in order to quantify pictures of vascular networks. I changed computer since that time, and now the dowlaod link I had does not work anymore. Does anyone still have angioquant on their computer ? Or another link to download the software ?
I thank you in advance for all the help you could provide.
Kind regards,
Sophia Coffy
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Hi Sophia,
I've looked into this for you and it seems that the AngioQuant software is no longer available. The website that used to host the software has been taken down and there is no other known link to download it.
I can suggest some potential avenues for locating the software or a suitable alternative.
  1. Contact the authors or developers: Try to get in touch with the creators of Angioquant or the researchers who have used it in their publications. They might be able to share the software with you or direct you to an active download link.
  2. Search online repositories: Sometimes, software like this is available on academic repositories or platforms like GitHub. Conduct a search using relevant keywords such as "Angioquant," "vascular network quantification," and "image analysis software."
  3. Explore alternative software: If you are unable to find Angioquant, you may want to consider alternative software solutions for analyzing vascular networks. Some of the popular ones include ImageJ (with the Angiogenesis Analyzer plugin), Vesselucida, and Vascular Network Analyzer (VAN). These tools offer various functionalities for quantifying vascular networks and may serve your needs.
  4. Post in relevant forums or social media groups: There are numerous online communities dedicated to discussing scientific software and tools. You may want to post your query in these forums or groups, as members may be able to share Angioquant or provide alternative recommendations.
I hope this information is helpful, and I wish you the best in locating Angioquant or a suitable alternative for your needs.
Kind regards,
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Python for Power System Analysis (PyPSA) is a free software toolbox for simulating and optimizing modern electrical power systems over multiple periods. PyPSA includes models for conventional generators with unit commitment, variable renewable generation, storage units, coupling to other energy sectors, and mixed alternating and direct current networks. It is designed to be easily extensible and to scale well with large networks and long-time series.
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Hi all,
Just to add to Adrian's answer. You might also be interested in this course: https://fneum.github.io/data-science-for-esm/intro.html.
It was developed by Dr. Fabian Neumann (part of the PyPSA group at TU Berlin) and is offered as part of the curriculum of the Department of Digital Transformation of Energy Systems at TU Berlin.
"On this website you will find practical introductions to many Python packages that are useful for dealing with energy data and building energy system models. [...] "
Table of content:
  • Welcome
  • Introduction to Python
  • Introduction to numpy and matplotlib
  • Introduction to pandas
  • Introduction to geopandas and cartopy
  • Introduction to rasterio and atlite
  • Introduction to networkx
  • Introduction to pyomo
  • Introduction to pypsa
  • Capacity Expansion Planning with pypsa
  • Preparation for Group Assignment
  • Sector-Coupling with pypsa
  • Interactive Visualisation and Dashboards
Best,
Viktor
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The one recommended by a researcher regarding (Dragon 5), its URL's has already being removed.
Kindly advise.
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What is the most complete free software in wind energy simulation ?
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Mohammed Igouzal There are various free wind energy modeling software solutions accessible, however the most comprehensive one would rely on your individual requirements and desires. Among the most well-known are:
1. OpenFOAM is an open-source computational fluid dynamics (CFD) program that may be used to simulate wind energy.
2. Elmer: An open-source multiphysical simulation program including a wind energy modeling module.
3. The National Renewable Energy Laboratory created FAST, a modular wind turbine modeling program (NREL).
4. WAsP: DHI's wind energy modeling program, which is widely used in the wind energy sector.
It's best to extensively explore and try each of these solutions to see which one is best for your individual use case.
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I have videos of C. elegans moving in 24-well plate. Is there any free software available which can analyze these videos to quantify worm movement and/or live-dead estimation? If someone knows, please help. Thanks.
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Thanks for your answer, Bharat. I will explore this tool.
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We are planning to use free software (Quantum Espresso, VASP or others) because of budget cuts and inability to buy commercial packs. So can we publish these calculations along with the synthetic part for explaining the results obtained?
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Completely normal. Quick search brought up many articles using Quantum Espresso specifically published in journals like Journal of Physics D and Physical Review B, even Physical Review Letters well above that impact factor range.
Many would argue that using free (open) code can be even preferable regarding the repeatability of the calculations.
Note that VASP requires a paid institutional license, but maybe you do have access to that.
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Hi all,
I want to ask what software do you usually use to develop your figures (for scientific papers). for better quality and save time
Personally i use Microsoft word or PowerPoint
I want to see if there is other better options
Many thanks
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I typically recommend my students to use Inkscape, as it is opensource and has a great community for help, https://inkscape.org/
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I'm searching for free software for the QMMM calculations of protein-ligand complexes. Kindly suggest.
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Hope you doing well
You can use Chem3D software a module of ChemDraw for QM/MM calculations.
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Hello all. I have recently updated my Mac OS and came to realise that some of the softwares that I have been using for my sequence alignment and editing are no longer compatible with the new version of OS. Any recommendations for alternatives for Bioedit and Clustal? Preferably free softwares for Mac. Thank you so much!
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UGene is a collection of tools for DNA analysis and includes Clustal as well
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I don't have a software to open this file can anyone suggest some online free software links
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Hello everyone
in my study, I will monitor and predict change in LULC. for monitoring change, I will use classification and change detection techniques but for predicting change, I don't have any idea how can i achieve it. can you please recommend to me any technique to achieve the predection of LULC : Free software or program
Thanks
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Thank you all for your response and interest. I have some ideas but I need more details. I think I will use the Markov chain to predict change in LULC but I need a suggestion for free software.
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How to analyze the XRD data with the RAS.data file, In Windows 10?
Please suggest free software or videos for this analysis
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Dear Leonardo Oliveira,
I mean to ask that , after completion of the XRD testing of the sample; as a result, we will get output from XRD testing as SAMPLE.RAS file. With that SAMPLE.RAS file, how can we get the chemical compositions of that particular sample?
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Dear all,
I am looking for a scientific tool wich be able to draw MOFs representative images. Do you recommend me any? Preferible free.
Thanks you so much in advance
Kind regards
Rosa
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Yes, I think Mercury is the best.
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Looking for recommendations of software to draw Thiessen polygons on a map. The points will be rainfall stations in the area.
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Is there any free software that can simulate pH dependence of adsorption of anions by carbonaceous materials?
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You want too much. Here maybe only experiment help.
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For statistical analysis and visualization of MS data
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I have done single crystal XRD of CsPbBr3 crystal and i need to draw x-ray rocking curve from that. is it possible to analyze the data using Origin? is there is any free software available for this?
The file types I got are . res; .hkl; .abs; .pcf files
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The Rocking curve function is available from IIT Bombay, Department of Physics. There you can send your sample for measurement. If you see better Laue diffraction oscillations it is the indicative of atomically smooth substrate-thin film and thin film-vacuum interfaces. In addition to this, oscillation may be symmetric or asymmetric depending upon on being the presence of the strain profile within the thin film layer Pratheek Mekkat
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How to analysis following ftir spectra, also send free software names to analyse FTIR spectra
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This does not look like a spectrum - it looks more like noise, which is supported by the very small variations of the intensity. Concerning a program to analyse FTIR spectra, what exactly would you like such a program to analyze - band assignment, spectrum identification or quantitative analysis?
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Hello. Can someone help me on how do I analysis this XRD result? I tried checking my result data using XRD library but the outcome is not as expected. Also, any recommendation on any free software that can be used to check the crystalline phases?
The sample of the data as attached. Thank you in advance.
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Origin and HighScore are not free. The only free XRD phase identification software I'm aware of is QualX2:
You may have to delete lines 1-31 in your data file to open it in QualX (just a guess, I can't test it right now).
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Hello researchers
Please suggest me any freeware for data analysis.
Currently i am using originlab software , with 21 days license. Any other software please suggest me
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Fellow researcher,
If you allow me the undeserved familiarity in my speech. Duuude, phyton and R are the best data analysis tools there is and both are free and have (freely available) tons of awesome tutorials.