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Questions related to Pipeline
Hello everyone,
I’m looking for a motivated collaborator to join an ongoing research paper focusing on applying Retrieval-Augmented Generation (RAG) pipelines to a novel real-world use case. The project explores advanced ML techniques for information retrieval and pattern detection with significant practical impact.
I’m seeking someone with:
- Experience in NLP, RAG pipelines, and anomaly detection
- Strong experimental and model development skills
- Familiarity with academic writing and publications
As for my background: I’m a Master’s student in Information Technology at Worcester Polytechnic Institute (WPI), specializing in data science and machine learning. My work includes SBERT-based innovation analysis, a Streamlit-deployed recommender system, and a RAG pipeline for legal document analysis. I also have published a research paper in IoT, available on my ResearchGate profile.
Currently, I am also interning for a marketing agency in Chicago where I am working on building sentiment analysis models to help drive their social media strategy.
I’m currently collaborating with a researcher who brings 2 years of work experience as a software engineer at a top tech startup in Europe, adding strong engineering expertise to our team.
This collaboration offers shared authorship on a high-impact paper and the chance to work on cutting-edge ML applications alongside passionate researchers.
If you’re interested, I’d love to connect and discuss further.
Best regards,
Harsh Deshpande
I want to search for articles about fluid-structure interaction in pipe leakage problems.
An existing pipeline, designed under ASME B31.4 is planned to be converted to transport multiphase commodities, natural gas and crude oil at the same time. Besides reviewing what's applicable on the gas side, ASME B31.8 standards, is there any special conditions that should be considered for this analysis?
Check at our new paper on 'MLOps: Automatic, Zero-Touch and Reusable Machine Learning Training and Serving Pipelines' that won the Best paper award at the 2023 IEEE International Conference on Internet of Things and Intelligence Systems (IoTaIS 2023) held in Bali, Indonesia.
Link to the Published Paper: https://ieeexplore.ieee.org/abstract/document/10346079
ResearchGate Paper Draft Link:
Conference Paper MLOps: Automatic, Zero-Touch and Reusable Machine Learning T...
This work demonstrates how an AI/ML model can be taken to production very easily using components from the Acumos AI project and do much more by creating zero-touch ML model infrastructures using Acumos and Nifi.
In our process, instead of using any heat exchanger, we are planning to cool the process stream using ambient air by 150 deg C. It would be very helpful if someone can suggest guideline for the same. The main concentration is on how to calculate the temperature drop if the process pipe is left bare open in the atmosphere without any insulation.
Hello everyone, I am conducting a simulation task using CEL method in Abaqus related to offshore pipeline. I would like to know how to assign different soil materials for several soil layers of Eulerian part in Abaqus, please help. Thank you so much
Hi everyone, I hope you all are fine, I have acoustic data from five different sensors for an underground pipeline. I want to compute the velocity. Can someone give me some suggestions and solutions on how to compute the velocity for all these five sensor data?
Looking forward to your responses!
Thank you all!
In terms of CFD, we often analyze the stability of the error using Von-Neumann analysis, especially for FDM based problems. Should we follow the same approach for a compressible fluid flow using FVM ?
Pigging is basically a cleansing process followed in all pipeline industries after the product has been delivered. There are many types of pigs that are inserted inside the pipeline for this process. After the cleansing has been done the product stains will remain in that pig. So, i basically need to check the residues that are there in the pig after the operation. Has anybody done this analysis in their industry, kindly share the parameters required for it.
Hi,
I am developing Deep learning model(s) for a binary classification problem. The DL works with a reasonable accuracy. Is there a reliable way to extract features from DL models built with 'Keras' pipeline? It seems that the feature contribution are distributed among several layers.
Thank You,
Partho
Thank you in advance to all the specialists in the field of environmental engineering in oil fields - the bioprocessing of petroleum oil hydrocarbons. I would like to share our experience in waste management of produced water and oil sludge. We will undertake a project to construct an evaporation pond for waste crude oil and polluted produced water, entitled: Reclamation of waste crude oil and soil treatment of the resulting water evaporation pit site.
The multi- project's objectives are to remediate hydrocarbon-contaminated soils for all pits, reclaim productive water pits in operation, including dry pits used in the past, close all productive water pits, and manage waste in accordance with Environmental Protection Agency (EPA) approved methods and international standards. The project's scope also includes the construction of two new evaporation pond facilities and new concrete water pipelines connecting all GOSPs to new evaporation ponds to transfer the produced water to new ponds.
I desire and ask to know about implementing unique projects that include the construction of new evaporation ponds and cement pipelines to connect them to the evaporation ponds, water produced in accordance with environmental engineering standards. If you have previous projects, I hope you share the experience of the implemented cases or any other web sources i.e. engineering standards or design of new evaporation ponds, case studies with associated waste reports. Knowing that the project site is in the onshore oil fields (desert). Please, if anyone has information that they would like to share or send, I would be grateful for your efforts and participation. This project will include studies and publications in distinguished and esteemed scientific journals.
I am a PhD student working with human plasma looking to do miRNA-seq analysis (differential gene expression, isomer analysis and isolating the best housekeeping genes within a cohort).
I'm keen to do the analysis myself, but after doing a lot of literature searches (and YouTube tutorials) I am really struggling to do so.
Does anyone know of a useful contact, course or information pack that will help me successfully complete the pipelines? Thanks in advance!
How to create a mean model per genotype from μCT scans (dicom or tiff input format) coming from different animals so we can later compare the two different population mean models.
Currently the pipeline that we use is as following:
We use a morphometric technique based on landmarks, take the DICOM file and create the 3D model using 3D Slicer. Then we place the landmarks in idav landmarks software with the aim to obtain the 3D coordinates and build the matrix and perform the form/shape analysis.
We are also able to compare the surface of two 3D models using 3D Slicer IGT extension, however we will like to be able to compare not only two animals but several more. Does anybody can recommend a way to go or any other extension or freely available software that we can use?
Or any file that we can modifiy in the command line to manually calculate the mean or surface or volumes to get the mean of the population?
Thanks in advance looking forward to reading all your suggestions!
Kind regards,
Mar
Dear All,
In my lab, we have performed whole-exome sequencing of 10 patients to see if we found any germline variations associated with prostate cancer.
I am new to projects that use sequencing and am a little lost on how to analyze these results.
Can anyone suggest to me an app, approach, or pipeline to analyze these results?
I have my data in fastq files and understand a little bit of R.
Thanks a lot
Hi everyone,
Let me introduce my data:
I am analyzing the single-cell RNA seq dataset. I'm gonna find the differential expression (DEGs) from different conditions in each cell type.
In addition, I'm working with Seurat's pipeline. My data is not suitable for pseudo-bulk DEGs analysis, therefore, mixed-model (MAST) is now my choice!
My question is, why do we need to use the normalized data (Scran-normalized, Log-normalized data) as the input of the MAST test, although the MAST test itself has the normalized method for count-depth (by cellular detection rate - CDR)?
I am working with tagseq data that I am aligning to a reference transcriptome of an organism. I used several approaches to produce a transcriptome: using Braker annotation pipeline (with reference genome and RNAseq data), Maker annotation pipeline (also with reference genome and RNAseq data) and de novo SPAdes RNA assembler (with RNAseq data only). Braker showed much higher Busco scores for annotated transcriptome than SPAdes assembly (so did Maker). However, when I align tagseq reads to the Braker or Maker transcriptome I get less than 20% of reads alignment rate. When I align the same reads to SPAdes assembly, the alignment rate is ~80%. This tells me something is wrong with the annotation (regardless of the tool - Braker or Maker). Has anyone run into a similar problem or has ideas why I am getting such a different results for predicted vs assembled transcriptomes?
How can end-to-end workflow automation be achieved for cloud-based machine and deep learning pipelines?
As OCT creates many downstream issues in the RNA analysis pipeline, has anyone tried thawing OCT tissue (smallish pieces) in prechilled (-20C) RNALATER-ICE? Since OCT is water soluble shouldn't the RNAlater remove most of it (provided you have at least 10 volumes) and still relatively maintain RNA integrity (by also increased extraction efficiency?)
I am new to understanding the transient and steady state analysis of the natural gas pipeline grids. Are there any articles/textbooks that can be suggested which explain about the steady state and transient nature, the gas flow differential equations and how to discretize them?
Hello Researchers,
To conduct fracture toughness tests for pipeline material how do you machine specimen using pipelines with small thicknesses (ex 7mm)?
According to ASTM E399, how do you satisfy the ligament length condition with a smaller specimen?
Thank you
hey guys, I'm working on a new project where I should transfer Facebook ads campaigns data to visualize in tableau or Microsoft power BI, and this job should be done automatically daily, weekly or monthly, I'm planning to use python to build a data pipeline for this, do you have any suggestions or any Resources I can read or any projects similar I can get inspired from ? thank you .
Due to low flow velocities, there are chances of water and deposits separating in the crude oil pipelines with substantial BS&W content which might leads to corrosion in CS pipelines. Is there any literature specifying guidelines for the minimum flow velocities available?
I need help modelling horizontal BNWF with axial, transverse, and vertical (bearing & uplift) springs and spring damper at the ends to simulate connectivity.
I want to know how I can model these on to the beam and assuming the pipeline segment is 1 kilometer in length, at what intervals should the soil springs be applied? Can we assign line springs in OpenSees?
Thank you
P.S I would like to validate my results through this paper "Seismic risk assessment of buried steel gas pipelines under seismic wave propagation based on fragility analysis - Vahid Jahangiri, Hamzeh Shakib" - DOI 10.1007/s10518-017-0260-1
I am looking for information or a database for recording repair, inspection and failure costs of gas pipelines.
The end of the HCP-MEG pipeline has cifti files that are already parceled out onto the Yeo 2011 resting state networks. However, the cifti files just have 107 spatial points, I cannot find what number correlates to what part of the Yeo parcellation. Does anyone have the answer so I can see what index is related to what part of the Yeo parcellation?
When I use the DAMASK pipeline in DERAM.3D software, I do not know where the grain orientation corresponds ? And what orientation of the grains corresponding to the '.txt ' file I added through the ODF window ?
RNA from soil will be isolated with Qiagen kit, sequencing will be fine with Illumina 2x150nt.
I am looking for a way to predict Transcription Start Site (TSS) in Aedes genome, Is there is any bioinformatics software or pipeline to predict TSS from genome sequence or a gene
Hi everyone,
My project is about the evolution of chemosensory genes in Hawaiian Drosophila. My data is already assembled and masked. I'm wondering which gene annotation pipeline is best for my project? Some people recommended MAKER. Is this the common pipeline that every use? This is my first time doing gene annotation so any advise is much appreciated. Thank you in advance!
Hi all,
I'm busy building a shiny analysis pipeline to analyse protemics data from mass spectrometry, and I was wondering what the exact difference is between the terms Over-represented, and Upregulated. Can they be used interchangeably? Is one more appropriate for RNA or proteins?
Thanks,
Sam
Hello world,
I am a researcher from India. Currently, Pursuing my Ph.D. in Marine Genetics from CSIR-NIO, India.
I want to develop a pipeline to analyze the raw DNA Sequences(WGS) using R or Python or Linux or Pearl language.
If anyone is interested, it will immensely help me.
Early leak detection in an offshore hydrocarbon pipeline is critical for ensuring the safety of personnel and the environment. However, it is challenging to achieve effective leak detection without false alarms, as a variety of factors can cause false alarms, such as changes in temperature, pressure, or flow rates, as well as instrument malfunction or even marine life interference.
Several technologies are available for early leak detection in offshore pipelines, including acoustic, thermal, and optical sensors, among others. Each technology has its strengths and limitations, and the most effective solution may depend on various factors, such as the pipeline location, operating conditions, and type of hydrocarbon being transported.
One approach to minimizing false alarms is to use multiple sensors and incorporate them into a comprehensive leak detection system that can analyze data from different sensors and cross-check the results to reduce false alarms. Additionally, regularly testing and maintaining the sensors and system can also help to minimize false alarms and ensure that the system is functioning effectively.
Ultimately, achieving effective early leak detection without false alarms in offshore hydrocarbon pipelines requires a combination of appropriate technology selection, system design, and regular maintenance and testing to ensure optimal performance.
Please elaborate on your opinion on it.

Due to the constraint of sample, I cannot re-collect the leaves from a genotype that was used for NGS analysis (can only produce draft genome) before. To improve that assembly, can I use the NGS data generated from another genotype (same species but apparently have high heterozygous rate compared to the old one)? If so, please advise for appropriate tool/pipeline and papers dealing with the same issue.
With my appreciation.
I want to investigate about flow rate changes inside a pipeline in a domestic area, I have searched for the amount of flow rate changes in the pipeline, but I have not found any paper on this subject.
If someone could introduce a paper or chapter of a book on this subject, I would greatly appreciate it.
#flow_rate #pipeline
I've been trying to know more about bioinformatics pipelines for whole genome shotgun sequencing data to use for the samples of animal fecal microbes diversity and identify pathogenic microorganisms (both of DNA and RNA).
what is the conditions of flowrate in pipelines of crude oil for wax deposition.how to increase or decrease the flowrate to remove wax from pipelines of crude oil. give me the formula for flowrate.
Hello, someone can help me with information about technology, device or methodologies for inspection, monitoring and repair of damage to pipelines located in subfluvial crossings, pipe installed under a water source (River usually) with difficult access
Greetings everyone. I have a png with highlighted areas and I need to convert it into a shapefile with all the pipelines as polygon features. Any help is appreciated.
Hello Expert
Can Anyone suggest the subareal debris flow impact on oil and gas pipeline?
Hydrodynamic loading or debris flow hazard interaction with pipeline?
Hello,
I am rather new to the computer aided engineering & design domains and are currently learning the basic techniques how to model, simulate and post-process a model. I learned that the typical pipeline seems to be modelling in CAD -> generating Tet-Mesh -> Simulation using FEM -> Post Process. For design changes, the pipeline is repeated.
Recently, I stumbled across the isogeometric analysis (IGA) method initially proposed by Hughes et al. [1] in 2005, which allows for FEM-like simulation in CAD. This relieves engineers from meshing that can account for up to 80% of development time [2] and shortens the design pipeline/cycle.
Now, many years have passed since 2005 but still the workhorse of computational engineering projects seems to be the FEM. So, I am curious why is IGA not more common in the industry, while it has so much potential? In order to better understand why the situation still is what it is, I would like to read about your opinions.
Lets boil it down to 2 questions:
1) Why is the IGA not more common in the industry?
2) Is the IGA eventually going to replace the FEM?
I would very much appreciate to read about your experiences and opinions :)
Best regards,
Daniel
[1] HUGHES, Thomas JR; COTTRELL, John A.; BAZILEVS, Yuri. Isogeometric analysis: CAD, finite elements, NURBS, exact geometry and mesh refinement. Computer methods in applied mechanics and engineering, 2005, 194. Jg., Nr. 39-41, S. 4135-4195.
[2] COTTRELL, J. Austin; HUGHES, Thomas JR; BAZILEVS, Yuri. Isogeometric analysis: toward integration of CAD and FEA. John Wiley & Sons, 2009.
I have the scRNAseq data sequenced by BGI, which can be processed by cellranger. but the result always show "Low Fraction Reads in Cells" as the fig showed
does any know the reason, I also tested my pipeline with 10X test data, result is ok
is there with any mistake I made or some bug between BGI and cellranger

Is there a solution for liquid hydrogen and gas hydrogen transmission line leakage?
What is your suggested software for simulating the hydrogen transfer process in pipelines?
I need to make publication ready figures from the network data generated by MENA pipeline. R package is also okay!
The pipeline conveys liquid from a high peak and then down. If the fluid is discharged by gravity from one side of the pipe, is it possible to crumple the pipe due to the negative pressure at the tip of the peak? How can you calculate the pressure difference required to destroy the pipe at the top?
By draining how much volume of fluid at the bottom of the peak, the pipe may be damaged in the peak?
Soon I will have to analyze some ATAC-Seq data, I was evaluating the pipelines currently available ... that it is simple to install (maybe conda) and to use ...
I was considering:
Or
Or
Any experiences or suggestions?
Dear all,
I am looking for a user-friendly pipeline for metagenomics analysis using COI (Cytochrome oxidase I) as marker. I have tried some of them based on python and computed by docker but is not enough clear to be used with students. Could anyone recommend me any alternative?
Thank you in advance.
I'm beginning a research paper on the Eastern Mediterranean Pipeline's effect on the economy of Israel, Greece, and Cyprus. What would be a good way to phrase this question?
Dear all,
I have been doing research on the leak detection of pipelines for some time. I did the simulations with simcenter software. But unfortunately, I tried to detect the location of the leak using Kalman filter in different ways, but it is not possible. Is it possible to guide me? Is it possible to send me the MATLAB code so that I can try on my own water pipelines and simulations?
I have completed my bachelors and masters in the medical field. I don’t have a great CGPA because my University doesn’t give much marks to our students. 72% is the highest in my field (Gold medalist), and I have 70.625% (Silver medalist). How do I pitch this point to the Universities?
Also I have 5 PubMed indexed publications (with 6 more in pipeline)
My IELTS score is 8 overall (L 8.5, R 9, W 7.5, S 7.5)
Do I have a shot at Ivy League institutes for a PhD?
I have RNA that is going to be used on the ONT (Nanopore) technology pipeline and my RNA is too dilute. Is there a protocol to dry/pellet the RNA in solution and then re-suspend the RNA in at a lower volume?
I am a young bioinformatics student, want to have clues for my project pipeline. hints and expert answers are welcome. THANKS
I want to calculate Steel pipeline corrosion rate in different conditions, so Which software is best for estimating of pipeline corrosion rate?
Hi, I am new to bioinformatics. My project involves Next-generation sequencing to look at differential gene expression of treated and untreated cells. I found that many papers have different methodologies. Some paper uses Linux but I am not good at it. Can anyone suggest a standard pipeline that uses R studio on Windows PC? Your valuable suggestion will be greatly appreciated.
Is it possible to calculate with following given data? outlet temperature and pressure of steam, capacity of boiler, Diameter of pipeline.
I am pursuing Ph.D. on anthropogenic impact on fluvial environment. This is my last year my work is almost complete. Can anyone walk me through the process of pursuing PDF in India or preferably abroad? I have one international publication in springer on water quality and two other are in the pipeline on river migration process and anthropogenic impact on rivers.
Hello everyone,
If I have a sequence of a protein in fasta format (or any other), how can I find which structures exist for the exact match or similar sequences programmatically? Is there any Python package that can do it?
PS: I am aware that you can do it with web servers like uniprot but what I look for is mostly a command-line tool that I can integrate into a pipeline.
Any help is appreciated.
Mustafa
I have to simulate a pipeline which is API 5L X60. I've been searching in the literature and I didn't find anything.
I'd like to ask if anyone can provide me with any papers or information on this subject.
Please, I am looking for dataset (that has flow, heat. temperature, knock, pressure, and any other parameters data in oil pipeline) that I can use for the purposes of leakage detection and its location using machine learning.
I need to evaluate the eigen frequency of pipeline using abaqus. adding deadload of fluid in the pipe is problematic for me. during frequency analysis no load is allowed to act.
as i had done this in ansys so how can i verify my result as my project head said to verify whether it is correct or not please help
Hello All,
Let's say I have a pipeline connecting to the outlet of a blower. The pressure at the blower outlet and thus the inlet of pipeline is 1500Pa. The pipeline is only subject to major and minor head loss and the loss due to change of elevation. The diameter of the pipeline is constant.
When I calculate the pressure drop along the pipeline, I found the pressure drop is 2500Pa. Meaning to say, the pressure at the end of pipeline is around -1000Pa. Is this possible to happen? Does gas able to flow along the pipeline and flow out at the outlet? What is the impact to the gas and pipeline?
Good morning,
Please I have an issue with my run and I need some help.
We did a metagenomic 96 sample run on Minion Mk1B (short-read 16S 400bp amplicons). The run lasted for 72 hours. Output was 9.7 gigabases (FAST5 files are 241GB). After this base-calling was initiated.
After 24 hours, the base calling was only 17% at which we aborted the base calling to do it on our server.
After 4 days now and only less than 20% is done. Why is it taking so long? We are using guppy v5.
What is the expected output size for such runs?
Does analysis usually take this long?
Is there a time limit by which we should stop the runs?
Thank you in advance.
Dear scientists
Our team sequenced the human whole-genomes for breast cancer genes analysis. We could manage to generate up to the VCF files. Now we want to annotate the data and do the KEGG pathway analysis the find out the networking of the genes. Anybody can show us the necessary pipeline along with the basic tools to solve the problem?
Thanks in advance.
How do i go about simulating a pipeline network with simscape/simulink to measure parameters pressure and flowrate in case of leakage. Any guidance or tutorials will be appreciated.
Can anyone help to check whether the major head loss calculation for the attached pipeline is correct? Kindly advise. Thanks!
Inclined uphill portion:
Length, L= 5.68m
Diameter, D=0.5984m
velocity, v= 17.62 m/s
surface roughness / Diameter, e/D =0.000250668
Re=4.08E+05
friction factor, f =0.0165
Pipeline Inclined angle = 70 deg
So,
Head loss=[ f*(L/D)*(v^2)/(2g) ] + L*sin (70 deg) =6.874042435 m
Straight Horizontal portion:
Length, L= 9.8m
Diameter, D=0.5984m
velocity, v= 17.62 m/s
surface roughness / Diameter, e/D =0.000250668
Re=4.08E+05
friction factor, f =0.0165
Pipeline Inclined angle = 0 deg
So,
Head loss=[ f*(L/D)*(v^2)/(2g) ] =4.276014958 m
Inclined downhill portion:
Length, L= 5.68m
Diameter, D=0.5984m
velocity, v= 17.62 m/s
surface roughness / Diameter, e/D =0.000250668
Re=4.08E+05
friction factor, f =0.0165
Pipeline Inclined angle = 70 deg
So,
Head loss= [ f*(L/D)*(v^2)/(2g) ] - Lsin (70 deg) = -1.917355708m
Total head loss= 6.874042435 m + 4.276014958 m - 1.917355708m
Total head loss=9.232702 m
What is the latest pipeline to run the RNA-Seq genomic data ?
HI guys,
I have heard many reasons that researchers do not want to move to cloud for their analysis. I definitely see cost being one of the challenges - which is being currently worked out.
With pipelines/workspaces and data available on the cloud- what could be improved for better use of cloud between labs/institutes for genomic analysis.
Mamta
A research on corrosion prediction in a gas pipeline using artificial neural network is the core interest. This time, an experimental data to model and train the ANN is required. Thanks in anticipation.
KH9 Hexagon images come in parts as (a) and (b), without any georeference. Manually georefrencing two parts in ArcGIS is giving a considerable error. The Heximap pipeline is not working with the images freely available from USGS as Declasss2. How do i stitch those images for further processing?
The main goal behind this question is extracting the best practices on how to establish a Data Science / IA Project.
Anyone would be generous to share with us the set of tools or even a boilerplate that may help or guide anyone working in the field and applying data science & IA to any domain.
Hello,
I am new in this field. I am doing metagenome analysis with shotgun reads. All reads are single ended. DNA was obtained from airways of human. I just want to find taxon abundances in the samples. Then I will predict the diversities and core microbes.
My mapping results are terrible. How can I handle bad mappings?? OR should I change the tools that I used the analysis?? Which tools are more accurate or sensitive for microbiome analysis?? I need any suggestions, please!
I followed this pipeline:
- Assembly was done using Megahit
- Short contigs (<200 bps) were removed using prinseq
- Read mapping against contigs was performed using BWA
- Similarity searches for GenBank, KEGG, , eggNOG were done using Diamond
- Binning was done using MaxBin2
You can find my mapping results in the attachment.

I need a brief explanation of pipeline flow conditions that the Darcy-Weisbach equation can be applied and how this application carried out?
The area in question has recorded several oil spill events in recent times due to pipeline vandalization of both crude and refined petroleum hydrocarbon products. Depth to water level is about 9 m. Groundwater samples were collected from hand dug wells and motorized boreholes. In both type of wells, dissolved organic carbon concentrations ranged between 15 to 53 mg/L while the redox potential ranged between + 21.4 to + 587.4 mV
With many literatures and tools of bioinformatics to analysis single cell RNA data, I would like to ask if there is a complete pipeline for all the process of the analysis. It includes a downstream steps of co-expression network constructions within R programming.
i have a project to do the vibration analysis of underwater pipeline hence i dont know from whee to start and how to do please help
I will be thankful for you if you share your knowledge with me and suggest the best coating process if we use Nick (Inconel 718) as as inner coating process in oil pipeline.
Does any one have good pipeline for analyzing bacterial RNA seq data using R? I found many pipelines and tutorials using eukaryotic data, but it is very tough for bacterial sequencing data.
Hello,
I am trying to preprocess DWI data for the first time in order to extract diffusion parameters and to perform tractography. I have watched all the tutorials provided by the Analysis Group (FSL), Andrew Jahn videos on Youtube and I have studied the DTI pipeline. However, I still have questions.
It is not very clear if I should preprocess my T1 data too. I am using it to perform registration with my diffusion images. I know that I should extract the brain (Bet function) but I was questioning about possible others steps I am missing? I am afraid it could bring artefacts onto my results.
Thank you for reading me,
Suppose there is a leak in a crude oil pipeline, after which the inlet valve of the line will be closed. However, depending on the length of the pipeline, it may take some time for the current in the ruptured section of the pipeline to be completely cut off. I am trying to calculate the flow rate change at the rupture location of the pipeline. (in my case pipe line length from leak to valve in about 25 km)
Different sources such as "OCS Study MMS 2002 - 033" have presented different equations to calculate the amount of leakage, but the results obtained from these equations in the best conditions calculate the amount of leakage after closing the valve equal to half the volume of the pipeline. It should be noted that none of these equations take into account the slope of the pipeline, which is also based on the events that have been recorded. It should be much less than half the volume of the pipeline. Does anyone have more information on how to accurately calculate the amount of leakage? It should also be noted that due to the very long length of the pipeline, it seems impossible to use CFD model. (I tried fluent)?
Thanks
There are many drag reducing agents suggestested for oil pipilines, I would like to know which one is more applicable?
Dear all,
I'm relatively new to the "ATAC-seq technology", I performed an ATAC-seq experiment using different cell lines (non transformed and cancer cell lines) and recently I received the sequencing (Raw) data.
I will be very grateful if you can share with me tutorials/reviews or useful links in order to analyze my ATAC-seq data (python or R scripts, pipelines.........)
Many thanks in advance
Karim
In some cases when I use black oil model the software stops solving the problem and warns that the pressure is beyond the range. I activated the slug tracking and problem is solved but when I want to run the pig there is a problem. how can I find out the cause of this error?
Hi all, currently I am working on Whole Genome Sequencing for some samples. Unfortunately, while performing the mapping process using bwa, the analysis retrieves me an error of
[M: :mem_pestat] skip orientation FF as there are not enough pairs
[M: :mem_pestat] skip orientation FR as there are not enough pairs
[M: :mem_pestat] skip orientation RF as there are not enough pairs
[M: :mem_pestat] skip orientation RR as there are not enough pairs
[mem_sam_pe] paired reads have different names: "E00534:137:H5KC7CCX2:1:1101:3488:1731", "E00534:138:H5KL3CCX2:1:1101:2493:1625"
Previously, I found one solution, suggesting running a repair.sh via bbmap/bbduk software however, I am not sure either I need to trim back the repair file via trimmomatic or just direct to mapping process after the repair/fixed process. Thus, here I would like to ask, what are others solutions that can I use to solve this mapping error and should I directly skip the trimming process via trimmomatic and direct to the mapping process.
I need Raman spectrums for develop data analytics pipelines to classifying chemical substance using Machine Learning techniques.
Hello. I would like to cut the surface of pipeline with girth weld to investigate the effect of residual stress on pitting corrosion. I am planning on adding bending force to the samples to make the situation more realistic, and I think I need flat samples to do so. Does anyone know how to cut the samples and flatten them while minimizing the effect on residual stress in the surface? Thanks in advance.
Dear All,
Which tool/software/script can extensively annotate bacterial genome with lower % of hypothetical protein annotates.
On annotation using PROKKA there are many sites without incomplete annotations. Is there a method/s or pipelines which help annotate such sites.
Any help would be really appreciated.
Thank you
Is there any relationship between the tendency of a gas to leak from containers/pipework and its molar weight?
For instance, given smaller molar mass of hydrogen (2.016 g/mol) compared to 16 g/mol for Natural Gas, is it correct to conclude that Hydrogen would exhibit a greater leakage risk when replacing natural gas in utility pipelines when transmitted under the same working pressures?
I am performing differential gene expression analysis using the CIRIquant pipeline. Referring to the CIRIquant cookbook, I successfully arrived into this step:
"Usage 3: Differential expression analysis - Study with biological replicates - Step3: Differential expression analysis"
However, there is an EdgeR error occurring (see below). Can someone explain to me what I may have done wrong?
Command used:
CIRI_DE_replicate --lib library_info.csv --bsj circRNA_bsj.csv --gene gene_count_matrix.csv --out circRNA_de.tsv
Log:
[Wed 2021-03-17 22:11:31] [INFO ] Library information: /home/andregabriel/Desktop/CIRI_test/library_info.csv
[Wed 2021-03-17 22:11:31] [INFO ] circRNA expression matrix: /home/andregabriel/Desktop/CIRI_test/circRNA_bsj.csv
[Wed 2021-03-17 22:11:31] [INFO ] gene expression matrix: /home/andregabriel/Desktop/CIRI_test/gene_count_matrix.csv
[Wed 2021-03-17 22:11:31] [INFO ] Output DE results: /home/andregabriel/Desktop/CIRI_test/circRNA_de.tsv
Warning message:
In estimateDisp.default(y = y$counts, design = design, group = group, :
No residual df: setting dispersion to NA
Error in glmFit.default(y = y$counts, design = design, dispersion = dispersion, :
Design matrix not of full rank. The following coefficients not estimable:
treatT
Calls: glmFit -> glmFit.DGEList -> glmFit -> glmFit.default
Execution halted
[Wed 2021-03-17 22:11:35] [INFO ] Finished!
I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff, star+stringtie+cuffdiff etc. However, among all the pipelines, only the Cuffdiff differential tool gave some genes with significant Q value whereas none others gave DEGs with significant adjusted P-value. So I would like to know from the people who are working with brain samples, what possible ways can be used for analyzing such data? What kind of adjusted P-value and log2fold change do you observe in your routine analysis?? Is there any specific normalization technique or pipeline for analyzing brain tissue samples??
Hi,
I am trying to analyse sequences produced using SMRT link from PacBio. My goal would be to produce asvs table and taxonomy as for a normal DADA2 pipeline, but I am struggling finding information about how to use the output sequences from PacBio in any bioinformatics pipeline.
Any suggestions?
P.s. still a newbie! ;)
I work with genetics and would like to ask if anyone can suggest any (drawing or figure) software tools suitable for making custom figures e.g. of pipelines, molecule interactions, DNA, RNA etc.
Any suggestions are appreciated, Thanks!
Optimization of hydrocarbon pipeline transportation and allocation using a pipeline network measurement system model
I am investigating the effect of velocity on severe slugging and this requires a CFD software that can simulate severe slug flow and at the same have the capacity to vary input velocities.
I have a dataset of eeg, sampled from children.
No electrodes attached to eyes area, so i can't use the function "reject data using ICA",
what is the best way to preprocess the data depending my situation?
In 16s rDNA metagenome analysis, after sequencing data. I want to classify bacteria based on their functions. I am looking for a Pipeline or any software that can do this job?
Hi Everyone,
I have acquired some plant hyperspectral images (roots, fruit, leaves) from various environmental conditions and now want to explore the data cubes to detect possible differences and plan to study plant physiology and chemometrics in future. The built-in software with the camera (Specim IQ studio) is not serving the purpose.
Any suggestion for easy-to-use and simple interface software or analysis pipeline for such exploration and making classifier models? Preferably open-source but commercial suggestions are also welcomed.
Many thanks in anticipation.