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OmicsSuite: A customized and pipelined suite for analysis and visualization of multi-omics big data

Abstract: Credit: Horticulture Research Abstract: With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics…




Credit: Horticulture Research


With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems, however it is challenging for most experimental biologists to analyze data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The multi-omics analysis functions were developed based on BioJava and 300+ packages provided by the R CRAN and Bioconductor communities, and it encompasses over 3,000 adjustable parameter interfaces. OmicsSuite can directly read multi-omics raw data in FastA, FastQ, MAF, mzML, Matrix, and HDF5 formats, and the programs emphasize data transfer directions and pipeline analysis functions. OmicsSuite can produce pre-publication images and tables, allowing users to focus on biological aspects. OmicsSuite offers multi-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants. It enables researchers to freely explore the molecular information contained in multi-omics big data (Source:, Website:, v1.3.9).

Brief Introduction:

Over the past decade, the widespread application of next-generation sequencing (NGS) technologies represented by Illumina Solexa and HiSeq platforms1, as well as third-generation sequencing (TGS) technologies led by PacBio Sequel2 and Oxford Nanopore3 platforms, has revolutionized the fields of molecular, evolutionary, and computational biology. Currently, omics diversity and integrated multi-omics analysis are thriving research fields, and multidimensional analysis of biological features and mechanisms has become more precise and efficient4. With the widespread application of sequencing and mass spectrometry technologies, the quantity and storage types of data generated are also rapidly increasing5. For example, data generated by PacBio HiFi sequencing has longer reads and higher throughput, and storage formats based on GC/LC-MS (Gas/Liquid Chromatography Mass Spectrometry) such as mzXML (mass spectrometric data in eXtensible Markup Language), mzData (mass spectrometric Data), and mzML6 are gradually evolving to meet more diverse needs. At the same time, data from 10X Genomics7, ranging from Chromium matrix data generated from single-cell transcriptomics to Visium HDF5 (Hierarchical Data Format version 5) data generated from spatial transcriptomics, have become more complex and mysterious. As a result, there are significant differences in the analytical pipelines, methods, and programs employed in data parsing for downstream bioinformatic analysis across genomics, transcriptomics, proteomics, metabolomics, microbial omics, and single-cell omics8.

Main Results:

OmicsSuite native framework architecture

OmicsSuite is an innovative framework for analyzing and visualizing multi-omics data in a workflow (Fig. 1). The JavaFX library provides user interface (UI) control methods, parameter component classes, web engine support, and other interface display and friendly interaction functions through a series of sub-libraries such as javafx-controls, javafx-graphics, and javafx-web. The interfaces and analysis parameters of all 175 sub-applications are implemented through various components provided by JavaFX. Each sub-application provides essential interfaces such as uploading example datasets or user data files, parameter synchronization and feedback, and outputting results. Rserve and REngine provided by org.rosuda.REngine ( as two special and critical libraries are used to implement real-time communication with the R environment through daemon threads. Correspondingly, the Rserve function is utilized to provide instant responses to Java call signals. Although OmicsSuite is used by Java and R as the real-time running environment and function execution environment respectively, and has a large number of built-in Java and R modules, and even the Shinyapp framework. But easily users only need to install based on binary file to use the full functionality out of the box, without any additional configuration environment and dependencies. Basically, a computer device with a 4-cores CPU, 4G memory, and 256G storage can perform normal operations of OmicsSuite. We recommend providing a minimum of 6-cores CPU and 8GB memory for single-cell analysis, with a test PBMC (Peripheral Blood Mononuclear Cells) dataset (including 2700 single cells) execution time of approximately 3 minutes.

UI design and data interface

OmicsSuite has redesigned the UI of JavaFX to provide a modern and improved operating experience for users. The default layout features a multi-level menu bar at the top of the window, a shortcut access bar at the bottom, a collapsible toolbox on the left, a home page in the middle, and a meta information and version update record panel on the right (Fig. 2A). The menu bar allows users to quickly launch sub-applications based on multi-level categorization. When a sub-application is started, the layout will switch to the user interface, with the analysis page of the application in the middle and application details information (Fig. 2B) on the right. The analysis page is comprised of a data section, a parameter component section, and a result section from top to bottom. The fixed components Progress, Demo, Clear, and Submit are part of the task management components used to display the current status, run example data, clear the current task, and submit a new task respectively. Other common components such as Themes, Colors, Fonts, Figure Width, Figure Height, and Figure DPI belong to the parameter specification components. These components implement a unified theme and color scheme for OmicsSuite and standardize the default output image in 10.00 × 6.18-inch (300 dpi) form, following the golden ratio.

Sub-applications overview and classification

Bioinformatics encompasses biology (such as multi-omics) and methodology (such as statistics and advanced algorithms). Therefore, OmicsSuite continuously improves multi-omics analysis and visualization functions based on the foundation of statistical analysis, providing users with a comprehensive one-stop solution. Currently, there are 12 categories with 175 sub-applications. The categories are: Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganisms, Single Cell, and Table Operation (Fig. 3). OmicsSuite can analyze almost all multi-omics data, and each classification corresponds to different types of professional data formats. Applications in the OmicsSuite Sequence category typically require a FastA format sequence file, applications in the Genomics category require data in MAF file (Mutation Annotation Format); applications in the Metabolomics category require compressed mzML format files, and users need to provide compressed Matrix or HDF5 format files for the Single-Cell category.

To summarize, the key features of OmicsSuite include: 1) User-friendly interactive experience, convenient demo running button, complete parameter components, and table and image preview windows. 2) Comprehensive coverage of multi-omics analysis and visualization functions, particularly in metabolomics and single-cell analysis workflows. 3) OmicsSuite supports reading most multi-omics raw files, such as LC-MS data mzML format, single-cell 10x genomics Chromium matrix format, and Visium HDF5 format data. 4) OmicsSuite provides a complete basic visualization system, intuitive operation interface for dimensionality reduction algorithms (PCA, PCoA, tSNE, etc.) and clustering algorithms (Kmeans, Hclust, AGNES, etc.), and a SEM model construction and evaluation system.

1 Caporaso JG, Lauber CL, Walters WA et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012; 6: 1621–1624.

2 Rhoads A, Au KF. PacBio Sequencing and Its Applications. Genomics, Proteomics Bioinforma 2015; 13: 278–289.

3 Jain M, Olsen HE, Paten B, Akeson M. Erratum to: The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community [ Genome Biol. (2016), 17, 239] DOI:10.1186/s13059-016-1103-0. Genome Biol 2016; 17: 95064.

4 Olivier M, Asmis R, Hawkins GA, Howard TD, Cox LA. The need for multi-omics biomarker signatures in precision medicine. Int J Mol Sci 2019; 20. doi:10.3390/ijms20194781.

5 Joseph LC, Shi J, Nguyen QN et al. Combined metabolomic and transcriptomic profiling approaches reveal the cardiac response to high-fat diet. iScience 2022; 25. doi:10.1016/j.isci.2022.104184.

6 Turewicz M, Deutsch EW. Spectra, Chromatograms, Metadata: mzML-The Standard Data Format for Mass Spectrometer Output. Methods Mol Biol 2011; 696: 179–203.

7 Gao C, Zhang M, Chen L. The Comparison of Two Single-cell Sequencing Platforms: BD Rhapsody and 10x Genomics Chromium. Curr Genomics 2020; 21: 602–609.

8 Fisch KM, Meißner T, Gioia L et al. Omics Pipe: A community-based framework for reproducible multi-omics data analysis. Bioinformatics 2015; 31: 1724–1728.

The article “OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data” has been published in Horticulture Research




Ben-ben Miao1,†,* , Wei Dong2,† , Yi-xin Gu4 , Zhao-fang Han1 , Xuan Luo1 , Cai-huan Ke1 , Wei-wei You1,3*

†These authors contributed equally to this work.


1. State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China.

2. Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou 510055, Guangdong, China.

3. Fujian Institute for Sustainable Oceans, Xiamen University, Xiamen 361102, Fujian, China.

4. College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China.

About Wei-wei You

Wei-wei You is a professor and doctoral supervisor at the College of Ocean and Earth Sciences, Xiamen University. Committed to the study of shellfish genomics and genetic breeding, and the response of marine shellfish to global change. He has published more than 180 academic papers as the first author, corresponding author or participating author in Reviews in Aquaculture, Molecular Ecology Resources, Aquaculture, Science of the Total Environment and other journals.

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United Airlines adds new flights to faraway destinations

The airline said that it has been working hard to "find hidden gem destinations."



Since countries started opening up after the pandemic in 2021 and 2022, airlines have been seeing demand soar not just for major global cities and popular routes but also for farther-away destinations.

Numerous reports, including a recent TripAdvisor survey of trending destinations, showed that there has been a rise in U.S. traveler interest in Asian countries such as Japan, South Korea and Vietnam as well as growing tourism traction in off-the-beaten-path European countries such as Slovenia, Estonia and Montenegro.

Related: 'No more flying for you': Travel agency sounds alarm over risk of 'carbon passports'

As a result, airlines have been looking at their networks to include more faraway destinations as well as smaller cities that are growing increasingly popular with tourists and may not be served by their competitors.

The Philippines has been popular among tourists in recent years.


United brings back more routes, says it is committed to 'finding hidden gems'

This week, United Airlines  (UAL)  announced that it will be launching a new route from Newark Liberty International Airport (EWR) to Morocco's Marrakesh. While it is only the country's fourth-largest city, Marrakesh is a particularly popular place for tourists to seek out the sights and experiences that many associate with the country — colorful souks, gardens with ornate architecture and mosques from the Moorish period.

More Travel:

"We have consistently been ahead of the curve in finding hidden gem destinations for our customers to explore and remain committed to providing the most unique slate of travel options for their adventures abroad," United's SVP of Global Network Planning Patrick Quayle, said in a press statement.

The new route will launch on Oct. 24 and take place three times a week on a Boeing 767-300ER  (BA)  plane that is equipped with 46 Polaris business class and 22 Premium Plus seats. The plane choice was a way to reach a luxury customer customer looking to start their holiday in Marrakesh in the plane.

Along with the new Morocco route, United is also launching a flight between Houston (IAH) and Colombia's Medellín on Oct. 27 as well as a route between Tokyo and Cebu in the Philippines on July 31 — the latter is known as a "fifth freedom" flight in which the airline flies to the larger hub from the mainland U.S. and then goes on to smaller Asian city popular with tourists after some travelers get off (and others get on) in Tokyo.

United's network expansion includes new 'fifth freedom' flight

In the fall of 2023, United became the first U.S. airline to fly to the Philippines with a new Manila-San Francisco flight. It has expanded its service to Asia from different U.S. cities earlier last year. Cebu has been on its radar amid growing tourist interest in the region known for marine parks, rainforests and Spanish-style architecture.

With the summer coming up, United also announced that it plans to run its current flights to Hong Kong, Seoul, and Portugal's Porto more frequently at different points of the week and reach four weekly flights between Los Angeles and Shanghai by August 29.

"This is your normal, exciting network planning team back in action," Quayle told travel website The Points Guy of the airline's plans for the new routes.

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Walmart launches clever answer to Target’s new membership program

The retail superstore is adding a new feature to its Walmart+ plan — and customers will be happy.



It's just been a few days since Target  (TGT)  launched its new Target Circle 360 paid membership plan. 

The plan offers free and fast shipping on many products to customers, initially for $49 a year and then $99 after the initial promotional signup period. It promises to be a success, since many Target customers are loyal to the brand and will go out of their way to shop at one instead of at its two larger peers, Walmart and Amazon.

Related: Walmart makes a major price cut that will delight customers

And stop us if this sounds familiar: Target will rely on its more than 2,000 stores to act as fulfillment hubs. 

This model is a proven winner; Walmart also uses its more than 4,600 stores as fulfillment and shipping locations to get orders to customers as soon as possible.

Sometimes, this means shipping goods from the nearest warehouse. But if a desired product is in-store and closer to a customer, it reduces miles on the road and delivery time. It's a kind of logistical magic that makes any efficiency lover's (or retail nerd's) heart go pitter patter. 

Walmart rolls out answer to Target's new membership tier

Walmart has certainly had more time than Target to develop and work out the kinks in Walmart+. It first launched the paid membership in 2020 during the height of the pandemic, when many shoppers sheltered at home but still required many staples they might ordinarily pick up at a Walmart, like cleaning supplies, personal-care products, pantry goods and, of course, toilet paper. 

It also undercut Amazon  (AMZN)  Prime, which costs customers $139 a year for free and fast shipping (plus several other benefits including access to its streaming service, Amazon Prime Video). 

Walmart+ costs $98 a year, which also gets you free and speedy delivery, plus access to a Paramount+ streaming subscription, fuel savings, and more. 

An employee at a Merida, Mexico, Walmart. (Photo by Jeffrey Greenberg/Universal Images Group via Getty Images)

Jeff Greenberg/Getty Images

If that's not enough to tempt you, however, Walmart+ just added a new benefit to its membership program, ostensibly to compete directly with something Target now has: ultrafast delivery. 

Target Circle 360 particularly attracts customers with free same-day delivery for select orders over $35 and as little as one-hour delivery on select items. Target executes this through its Shipt subsidiary.

We've seen this lightning-fast delivery speed only in snippets from Amazon, the king of delivery efficiency. Who better to take on Target, though, than Walmart, which is using a similar store-as-fulfillment-center model? 

"Walmart is stepping up to save our customers even more time with our latest delivery offering: Express On-Demand Early Morning Delivery," Walmart said in a statement, just a day after Target Circle 360 launched. "Starting at 6 a.m., earlier than ever before, customers can enjoy the convenience of On-Demand delivery."

Walmart  (WMT)  clearly sees consumers' desire for near-instant delivery, which obviously saves time and trips to the store. Rather than waiting a day for your order to show up, it might be on your doorstep when you wake up. 

Consumers also tend to spend more money when they shop online, and they remain stickier as paying annual members. So, to a growing number of retail giants, almost instant gratification like this seems like something worth striving for.

Related: Veteran fund manager picks favorite stocks for 2024

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President Biden Delivers The “Darkest, Most Un-American Speech Given By A President”

President Biden Delivers The "Darkest, Most Un-American Speech Given By A President"

Having successfully raged, ranted, lied, and yelled through…



President Biden Delivers The "Darkest, Most Un-American Speech Given By A President"

Having successfully raged, ranted, lied, and yelled through the State of The Union, President Biden can go back to his crypt now.

Whatever 'they' gave Biden, every American man, woman, and the other should be allowed to take it - though it seems the cocktail brings out 'dark Brandon'?

Tl;dw: Biden's Speech tonight ...

  • Fund Ukraine.

  • Trump is threat to democracy and America itself.

  • Abortion is good.

  • American Economy is stronger than ever.

  • Inflation wasn't Biden's fault.

  • Illegals are Americans too.

  • Republicans are responsible for the border crisis.

  • Trump is bad.

  • Biden stands with trans-children.

  • J6 was the worst insurrection since the Civil War.

(h/t @TCDMS99)

Tucker Carlson's response sums it all up perfectly:

"that was possibly the darkest, most un-American speech given by an American president. It wasn't a speech, it was a rant..."

Carlson continued: "The true measure of a nation's greatness lies within its capacity to control borders, yet Bid refuses to do it."

"In a fair election, Joe Biden cannot win"

And concluded:

“There was not a meaningful word for the entire duration about the things that actually matter to people who live here.”

Victor Davis Hanson added some excellent color, but this was probably the best line on Biden:

"he doesn't care... he lives in an alternative reality."

*  *  *

Watch SOTU Live here...

*   *   *

Mises' Connor O'Keeffe, warns: "Be on the Lookout for These Lies in Biden's State of the Union Address." 

On Thursday evening, President Joe Biden is set to give his third State of the Union address. The political press has been buzzing with speculation over what the president will say. That speculation, however, is focused more on how Biden will perform, and which issues he will prioritize. Much of the speech is expected to be familiar.

The story Biden will tell about what he has done as president and where the country finds itself as a result will be the same dishonest story he's been telling since at least the summer.

He'll cite government statistics to say the economy is growing, unemployment is low, and inflation is down.

Something that has been frustrating Biden, his team, and his allies in the media is that the American people do not feel as economically well off as the official data says they are. Despite what the White House and establishment-friendly journalists say, the problem lies with the data, not the American people's ability to perceive their own well-being.

As I wrote back in January, the reason for the discrepancy is the lack of distinction made between private economic activity and government spending in the most frequently cited economic indicators. There is an important difference between the two:

  • Government, unlike any other entity in the economy, can simply take money and resources from others to spend on things and hire people. Whether or not the spending brings people value is irrelevant

  • It's the private sector that's responsible for producing goods and services that actually meet people's needs and wants. So, the private components of the economy have the most significant effect on people's economic well-being.

Recently, government spending and hiring has accounted for a larger than normal share of both economic activity and employment. This means the government is propping up these traditional measures, making the economy appear better than it actually is. Also, many of the jobs Biden and his allies take credit for creating will quickly go away once it becomes clear that consumers don't actually want whatever the government encouraged these companies to produce.

On top of all that, the administration is dealing with the consequences of their chosen inflation rhetoric.

Since its peak in the summer of 2022, the president's team has talked about inflation "coming back down," which can easily give the impression that it's prices that will eventually come back down.

But that's not what that phrase means. It would be more honest to say that price increases are slowing down.

Americans are finally waking up to the fact that the cost of living will not return to prepandemic levels, and they're not happy about it.

The president has made some clumsy attempts at damage control, such as a Super Bowl Sunday video attacking food companies for "shrinkflation"—selling smaller portions at the same price instead of simply raising prices.

In his speech Thursday, Biden is expected to play up his desire to crack down on the "corporate greed" he's blaming for high prices.

In the name of "bringing down costs for Americans," the administration wants to implement targeted price ceilings - something anyone who has taken even a single economics class could tell you does more harm than good. Biden would never place the blame for the dramatic price increases we've experienced during his term where it actually belongs—on all the government spending that he and President Donald Trump oversaw during the pandemic, funded by the creation of $6 trillion out of thin air - because that kind of spending is precisely what he hopes to kick back up in a second term.

If reelected, the president wants to "revive" parts of his so-called Build Back Better agenda, which he tried and failed to pass in his first year. That would bring a significant expansion of domestic spending. And Biden remains committed to the idea that Americans must be forced to continue funding the war in Ukraine. That's another topic Biden is expected to highlight in the State of the Union, likely accompanied by the lie that Ukraine spending is good for the American economy. It isn't.

It's not possible to predict all the ways President Biden will exaggerate, mislead, and outright lie in his speech on Thursday. But we can be sure of two things. The "state of the Union" is not as strong as Biden will say it is. And his policy ambitions risk making it much worse.

*  *  *

The American people will be tuning in on their smartphones, laptops, and televisions on Thursday evening to see if 'sloppy joe' 81-year-old President Joe Biden can coherently put together more than two sentences (even with a teleprompter) as he gives his third State of the Union in front of a divided Congress. 

President Biden will speak on various topics to convince voters why he shouldn't be sent to a retirement home.

According to CNN sources, here are some of the topics Biden will discuss tonight:

  • Economic issues: Biden and his team have been drafting a speech heavy on economic populism, aides said, with calls for higher taxes on corporations and the wealthy – an attempt to draw a sharp contrast with Republicans and their likely presidential nominee, Donald Trump.

  • Health care expenses: Biden will also push for lowering health care costs and discuss his efforts to go after drug manufacturers to lower the cost of prescription medications — all issues his advisers believe can help buoy what have been sagging economic approval ratings.

  • Israel's war with Hamas: Also looming large over Biden's primetime address is the ongoing Israel-Hamas war, which has consumed much of the president's time and attention over the past few months. The president's top national security advisers have been working around the clock to try to finalize a ceasefire-hostages release deal by Ramadan, the Muslim holy month that begins next week.

  • An argument for reelection: Aides view Thursday's speech as a critical opportunity for the president to tout his accomplishments in office and lay out his plans for another four years in the nation's top job. Even though viewership has declined over the years, the yearly speech reliably draws tens of millions of households.

Sources provided more color on Biden's SOTU address: 

The speech is expected to be heavy on economic populism. The president will talk about raising taxes on corporations and the wealthy. He'll highlight efforts to cut costs for the American people, including pushing Congress to help make prescription drugs more affordable.

Biden will talk about the need to preserve democracy and freedom, a cornerstone of his re-election bid. That includes protecting and bolstering reproductive rights, an issue Democrats believe will energize voters in November. Biden is also expected to promote his unity agenda, a key feature of each of his addresses to Congress while in office.

Biden is also expected to give remarks on border security while the invasion of illegals has become one of the most heated topics among American voters. A majority of voters are frustrated with radical progressives in the White House facilitating the illegal migrant invasion. 

It is probable that the president will attribute the failure of the Senate border bill to the Republicans, a claim many voters view as unfounded. This is because the White House has the option to issue an executive order to restore border security, yet opts not to do so

Maybe this is why? 

While Biden addresses the nation, the Biden administration will be armed with a social media team to pump propaganda to at least 100 million Americans. 

"The White House hosted about 70 creators, digital publishers, and influencers across three separate events" on Wednesday and Thursday, a White House official told CNN. 

Not a very capable social media team... 

The administration's move to ramp up social media operations comes as users on X are mostly free from government censorship with Elon Musk at the helm. This infuriates Democrats, who can no longer censor their political enemies on X. 

Meanwhile, Democratic lawmakers tell Axios that the president's SOTU performance will be critical as he tries to dispel voter concerns about his elderly age. The address reached as many as 27 million people in 2023. 

"We are all nervous," said one House Democrat, citing concerns about the president's "ability to speak without blowing things."

The SOTU address comes as Biden's polling data is in the dumps

BetOnline has created several money-making opportunities for gamblers tonight, such as betting on what word Biden mentions the most. 

As well as...

We will update you when Tucker Carlson's live feed of SOTU is published. 

Tyler Durden Fri, 03/08/2024 - 07:44

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