Daniel J. Geiszler
Dec 1, 2020; 0:TIR120.002216v1-mcp.TIR120.002216
Technological Innovation and Resources

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You might receive a Segmentation Violation when opening a database table in SAS. The SAS Log contains the error and traceback:

In SAS Customer Intelligence, a decision campaign can become corrupted and impossible to open. When you try to open the campaign, an error message is displayed that asks you to check the SAS Customer Intel

Mass spectrometry has become an indispensable tool for the characterization of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. Although glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent approaches have not. This has significantly limited high throughput studies of unusual or atypical glycosylation events such as those observed in bacteria. As such, computational approaches to examine bacterial glycosylation and identify chemically diverse glycans are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach using N-linked glycopeptides of Campylobacter fetus subsp. fetus as well as O-linked glycopeptides of Acinetobacter baumannii and Burkholderia cenocepacia revealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses before database searching. Using this approach, we demonstrate how wide tolerance searching can be used to compare glycan use across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined, these results show that open searching is a robust computational approach for the determination of glycan diversity within bacterial proteomes.

Cross-linking MS (XL-MS) has been recognized as an effective source of information about protein structures and interactions. In contrast to regular peptide identification, XL-MS has to deal with a quadratic search space, where peptides from every protein could potentially be cross-linked to any other protein. To cope with this search space, most tools apply different heuristics for search space reduction. We introduce a new open-source XL-MS database search algorithm, OpenPepXL, which offers increased sensitivity compared with other tools. OpenPepXL searches the full search space of an XL-MS experiment without using heuristics to reduce it. Because of efficient data structures and built-in parallelization OpenPepXL achieves excellent runtimes and can also be deployed on large compute clusters and cloud services while maintaining a slim memory footprint. We compared OpenPepXL to several other commonly used tools for identification of noncleavable labeled and label-free cross-linkers on a diverse set of XL-MS experiments. In our first comparison, we used a data set from a fraction of a cell lysate with a protein database of 128 targets and 128 decoys. At 5% FDR, OpenPepXL finds from 7% to over 50% more unique residue pairs (URPs) than other tools. On data sets with available high-resolution structures for cross-link validation OpenPepXL reports from 7% to over 40% more structurally validated URPs than other tools. Additionally, we used a synthetic peptide data set that allows objective validation of cross-links without relying on structural information and found that OpenPepXL reports at least 12% more validated URPs than other tools. It has been built as part of the OpenMS suite of tools and supports Windows, macOS, and Linux operating systems. OpenPepXL also supports the MzIdentML 1.2 format for XL-MS identification results. It is freely available under a three-clause BSD license at https://openms.org/openpepxl.

Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multi-experiment comparisons for studying changes in modification profiles, e.g. in data generated in different laboratories or under different conditions. We demonstrate how PTM-Shepherd improves the analysis of data from formalin-fixed paraffin-embedded samples, detects extreme underalkylation of cysteine in some datasets, discovers an artefactual modification introduced during peptide synthesis, and uncovers site-specific biases in sample preparation artifacts in a multi-center proteomics profiling study.

Phillies pitchers and catchers have their first workout Wednesday morning at Carpenter Complex. Almost anything can happen between Wednesday and Opening Day. That said, here is a very early prediction of the Phillies' Opening Day roster, knowing the Phillies remain in the hunt to sign Bryce Harper or Manny Machado.

The Angels head to Spring Training with most of their roster set, but there will be competition for a few spots. Here's a look at the projected roster for the Angels, as they begin their first campaign under manager Brad Ausmus.

Spring Training is officially here for the Angels, with pitchers and catchers reporting to Tempe Diablo Stadium on Tuesday. And there's a new face at manager, with Brad Ausmus replacing longtime skipper Mike Scioscia this offseason.

Angels first baseman Albert Pujols met with the media for the first time this spring on Sunday and said he's fully healthy after undergoing arthroscopic surgery on his left knee in late August.

Members event (open ticket) 1 February 2023 — 9:00PM TO 10:00PM Anonymous (not verified) 1 February 2023 Chatham House and Online

Oct. 24, 2024 — The San Diego Supercomputer Center (SDSC), part of the School of Computing, Information and Data Sciences at UC San Diego, has been leading the Open Storage Network (OSN) program for years, and along […]

The post SDSC Leads Expansion of Open Storage Network to More Campus Computing Sites appeared first on HPCwire.

Oct. 16, 2024 — The ISC High Performance Jack Dongarra Early Career Award and Lecture Series is an annual event that honors the remarkable contributions of Professor Jack Dongarra to […]

The post ISC Opens Nominations for 2025 Jack Dongarra Early Career Award in HPC appeared first on HPCwire.

BEAVERTON, Ore., Oct. 29, 2024 — Ultra Accelerator Link (UALink) Consortium, led by Board Members from AMD, Amazon Web Services (AWS), Astera Labs, Cisco, Google, Hewlett Packard Enterprise (HPE), Intel, Meta […]

The post Ultra Accelerator Link Consortium Launches with Industry Leaders, Opens Membership to Drive AI Connectivity Standards appeared first on HPCwire.

June 24, 2024 — Haiqu, a quantum computing startup, announced the release of its new open-source toolkit – Rivet. This new toolkit is made to help developers streamline the execution of […]

The post Haiqu Releases Open-Source Rivet for Quantum Workflow Execution appeared first on HPCwire.

The movement toward open source AI made progress today when the Open Source Initiative released the first Open Source AI Definition (OSAID). While the OSAID provides one step forward, the […]

The post OSI Open AI Definition Stops Short of Requiring Open Data for LLMs appeared first on HPCwire.

FORT MYERS, Fla., Nov. 7, 2024 — The AlmaLinux OS Foundation, the nonprofit that stewards the free and community-governed open source enterprise Linux distribution, today announced that chair benny Vasquez is […]

The post AlmaLinux OS Foundation Chair to Discuss Embracing Diversity in Open Source at SC24 appeared first on HPCwire.

KAWASAKI, Japan and SANTA CLARA, Calif., Nov. 1, 2024 — Fujitsu and AMD have announced that they have signed a memorandum of understanding (MOU) to form a strategic partnership to […]

The post Fujitsu and AMD to Begin Strategic Partnership to Accelerate Open-source AI initiatives appeared first on HPCwire.

IBM and NASA have developed a new AI foundation model for a wide range of climate and weather applications, with contributions from the Department of Energy’s Oak Ridge National Laboratory. […]

The post IBM and NASA Launch Open-Source AI Model for Advanced Climate and Weather Research appeared first on HPCwire.

Red Hat has announced a signed agreement to acquire Neural Magic, a developer of software and algorithms that accelerate generative AI (gen AI) inference workloads. Red Hat mentions Neural Magic’s […]

The post Red Hat Acquisition Charts Path to Open Accelerated AI appeared first on HPCwire.

A team of U.S. employees at Hachette wrote an open letter to management in protest over a new conservative book imprint created in wake of last week's Donald Trump victory headed by a known far-right publisher.

Montana Superintendent Elsie Arntzen offers practical advice to schools that could open as early as May 7, even as she says "how they open schools and how learning takes place is up to them."

As Montana's governor pursues a plan to gradually reopen the state, the state education department is relying in part on public opinion to decide whether to reopen schools this year.

Maryland's state school board will allow noneducators to be appointed as superintendents of school systems.

School district leaders must make high-stakes decisions with woefully imperfect information.

Florida’s Gov. Ron DeSantis said on Monday that schools will be required to remain open despite the rise in confirmed COVID-19 cases and hospitalizations, arguing lockdowns and closures have not worked.

The change under consideration would make the reading test less accurate not more, writes E.D. Hirsch Jr.

With coronavirus cases surging, labor groups are continuing to flex their political muscle, most often pushing for a conservative approach to getting teachers and kids back in buildings.

Alabama lawmakers passed a charter school law last year, becoming the 43rd state to adopt one.

A K-8 charter school has opened in Livingston, Ala., that is making history.

School administrators in some states are caught up in tensions about who gets the final say about when they can reopen their buildings and what precautions they should take to protect their communities.

A state appellate court indicated it was likely to side with Florida Gov. Ron DeSantis and his administration's emergency order requiring schools to open for brick-and-mortar instruction.

Florida’s Gov. Ron DeSantis said on Monday that schools will be required to remain open despite the rise in confirmed COVID-19 cases and hospitalizations, arguing lockdowns and closures have not worked.

The school district, which serves about 11,200 students, postponed opening because of the protests following the death of Michael Brown, the 18-year-old black teenager who was shot by a white police officer.

School administrators in some states are caught up in tensions about who gets the final say about when they can reopen their buildings and what precautions they should take to protect their communities.

Lawsuits are percolating nationwide as state officials, parents, teachers, and others clash over how and whether school buildings should reopen amid the continuing pandemic.

Kansas State football coach Chris Klieman talks about what the Wildcats did during the open week ahead of their home game against Arizona State.

Kansas State football actually benefitted from an open week in the latest College Football Playoff rankings.