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Free Software - Science topic
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Questions related to Free Software
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?
or a link to any other free software or website that can be used to calculate combination index?
Kindly suggest any free software for scaffold hopping?? I have a pharmacophore and need its various possible derivatives.
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
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
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!
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
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).
What are free software to fit XRR data for thin film structure?
Is there any free software for caring out these calculations.
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?
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!
- Because there is many software but which one is best.
Could anyone suggested molecular dynamic analysis free software tools name and link?
Can you tell pros and cons of each fluorescence in situ hybridization free softwares? have you used it in impact articles?
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
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.
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
"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?"
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
Hello experts,
Does anyone know any free software about retention index prediction ?
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 !
A free software (web version)of blackbody radiation law is used through URL(http://39.105.188.151:3000/index)
To do life cycle impact assessment related with asphalt/asphalt production suggest me suitable software and databases please
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 :-)
I am trying to simulate a new solar cell which has almost 15 layers. But SCAPS has only 7 layers.
Please, can the fragmentation obtained from the mass spectrometry be predicted more easily using any free software? Kindly recommend it, thanks.
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!
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.
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?
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.
I know SoundPLAN and ODEON, but I want to know any free software. Thank you.
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?
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
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.
Actually I want to perform RNA seq analysis via NGS platform to identify the genomic variability and diversity in specific viral strains
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.
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.
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?
- 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?
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?
I want to free download software available to assess soil moisture budget using the Throtnwaite and Mather method
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?
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.
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
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.
For the measurement of particle size from XRD TEM SEM etc
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
Dear Colleagues,
Is there any free software for GPS Vehicle Tracking?
Regards
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?
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?
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.
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
I want to draw some patient pedigrees for a manuscript. Any suggestion for free software?
Hi,
I am working on analysis of a study where I need PSM matching . Kindly suggest a free software for PSM analysis. TIA.
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.
Please suggest me a free software to make conceptual and theoretical frameworks
In my study i am using nanocellulose based membrane for the adsorption study of dye and heavy metals
Free software to gather a tremendous amount of research material.
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.
For example, I want to capture on Facebook all pages or accounts three months ago communicated a particular event, say an Earthquake.
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.
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!
For solving chemical parameters of a single crystal, which softwares are helpful, in addition to that, which is good for doing docking analysis
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?
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
I heard about CANOCO but it isn´t free.
Hi everyone, any suggestion for free software for overlaying a DFT structure to an X-ray structure, please?
Thank you
Musa
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?
Do you know any alternative free software to draw flow diagrams?
Thank you in advance!
I am looking for free software work on the ocean optics spectrometer. I bough used one without software 2000+
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.
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.
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.
Monte Carlo
free software
cad design
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.
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.
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
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.
The one recommended by a researcher regarding (Dragon 5), its URL's has already being removed.
Kindly advise.
What is the most complete free software in wind energy simulation ?
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.
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?
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
I'm searching for free software for the QMMM calculations of protein-ligand complexes. Kindly suggest.
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!
I don't have a software to open this file can anyone suggest some online free software links
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
How to analyze the XRD data with the RAS.data file, In Windows 10?
Please suggest free software or videos for this analysis
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
Looking for recommendations of software to draw Thiessen polygons on a map. The points will be rainfall stations in the area.
Is there any free software that can simulate pH dependence of adsorption of anions by carbonaceous materials?
For statistical analysis and visualization of MS data
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
How to analysis following ftir spectra, also send free software names to analyse FTIR spectra

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.
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