Cytoscape.js 2023 update: a graph theory library for visualization and analysis

SUMMARY

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. This update describes new features and enhancements introduced over many new versions from 2015 to 2022.

AVAILABILITY AND IMPLEMENTATION

Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Abstract 1156: Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer

Interpreting genomic variants in tumor samples presents a challenge in research and the clinical setting. A major barrier is that information about variants is fragmented across disparate databases, and aggregating information from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, a one stop shop for variant annotation, equipped with a powerful API for bulk annotation of variants and a user friendly interface for cancer researchers.

Genome Nexus is available at https://www.genomenexus.org. It a) aggregates variant information from a large number of sources that are relevant to cancer research and clinical applications; b) allows high-performance programmatic access to the aggregated data via a unified API; c) provides a search interface and a reference page for individual cancer variants; d) provides user-friendly tools for annotating variants in patients; e) is freely available under an open source license and can be installed in a private cloud or local environment.

Genome Nexus contains annotations from more than a dozen resources, including those that provide variant effect information (VEP), protein sequence annotation (Uniprot, Pfam, dbPTM), functional consequence prediction (Polyphen-2, Mutation Assessor, SIFT), population prevalence (gnomAD, dbSNP, ExAC), cancer population prevalence (Cancer Hotspots, SignalDB) and clinical actionability (OncoKB, CIViC, Clinvar). The annotations can be accessed through the website, the API, and a command line client.

Genome Nexus is unique in providing a user friendly interface specific to cancer that allows high performance annotation of any variant. It is the main annotation service for the popular cancer genomics tool cBioPortal, which serves thousands of users daily. It is also offered as a standalone tool for annotation, allowing researchers and clinicians as well as genomic infrastructure developers to leverage it directly in their own workflows. For example, a local installation of Genome Nexus is used for annotating all variants in AACR Project GENIE.

Citation Format: Ino de Bruijn, Xiang Li, Onur Sumer, Benjamin Gross, Robert Sheridan, Angelica Ochoa, Manda Wilson, Avery Wang, Hongxin Zhang, Aaron Lisman, Adam Abeshouse, Sander Rodenburg, Sjoerd van Hagen, Remond Fijneman, Gerrit Meijer, Nikolaus Schultz, Jianjiong Gao. Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1156.

Effect of Tacrolimus on Peripheral Nerve Regeneration in Allograft Transplantation: A Light and Electron Microscopic Study

OBJECTIVES

Peripheral nerve injuries are common in Europe; however, the treatment techniques may lead to disabilities. This study aimed to evaluate the effect of tacrolimus use on the capacity of the epineural sheath graft to improve its regeneration quality in rat sciatic nerves as a treatment option for nerve injuries.

MATERIALS AND METHODS

In the experimental process, 30 male Sprague Dawley were used as recipients and 10 Wistar rats were used as donors. Under anesthesia, all rats were operated on to resect the sciatic nerve. The nerve tissue of Wistar rats was used as allograft. In the autograft group, the resected nerve was reversed and sutured, resulting in an epineural sheath graft. For the allograft groups, rats were randomly divided into 2 groups as the tacrolimus-treated group and the nontreated group after allograft transplant. Tacrolimus was administered intramuscularly at 0.1 mg/kg daily for 12 weeks. After the treatment period, rats were killed and evaluated histomorphologically with light and electron microscopy.

RESULTS

Histological examination showed no remarkable differences between different regions of the sciatic nerves (distal, middle, and proximal). The axonal density was decreased in the allograft groups compared with the autograft group (P < .001). Results showed that the number of mast cells was increased in the allograft group without tacrolimus treatment (P < .05). Similarly, there was a mild increase in mast cell count in the tacrolimus-treated allograft group.

CONCLUSIONS

Our results showed that tacrolimus use in rats with implanted epineural nerve sheath supported recovery in terms of morphological and physiological regeneration of the nerve.

Abstract 2607: The cBioPortal for Cancer Genomics: an open source platform for accessing and interpreting complex cancer genomics data in the era of precision medicine

The cBioPortal for Cancer Genomics is an open-access portal (http://cbioportal.org) that enables interactive, exploratory analysis of large-scale cancer genomics data. It integrates genomic and clinical data, and provides a suite of visualization and analysis options, including cohort and patient-level visualization, mutation visualization, survival analysis, enrichment analysis, and network analysis. The user interface is user-friendly, responsive, and makes genomic data easily accessible to translational scientists, biologists, and clinicians.

The cBioPortal is a fully open source platform. All code is available on GitHub (https://github.com/cBioPortal/) under GNU Affero GPL license. The code base is maintained by multiple groups, including Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, and The Hyve, an open source bioinformatics company based in the Netherlands. More than 30 academic centers as well as multiple pharmaceutical and biotech companies maintain private instances of the cBioPortal. This includes the recently launched cBioPortal instance at the NCI Genomic Data Commons (https://cbioportal.gdc.nci.nih.gov/), and two large cBioPortal instances hosting genomic and clinical data at MSK and DFCI, supporting the MSK-IMPACT and DFCI Profile projects, two of the largest clinical sequencing efforts in the world.

Our multi-institutional software team has accelerated the progress of evolving the core architectural technologies and developing new features to keep pace with the rapidly advancing fields of cancer genomics and precision cancer medicine. For example, we have integrated multi-platform genomics data with extensive clinical data including patient demographics, treatment history, and survival data. We have also developed a patient-centric view that visualizes both clinical and genomic data with annotation from OncoKB knowledge base. In the next few years, the development team will focus on the following areas:

(1) Implementing major architectural changes to ensure future scalability and performance.

(2) New features to support precision medicine, including (i) improved integration of knowledge base annotation, (ii) enhanced visualization of patient timeline, drug response, and tumor evolution, (iii) new patient similarity metrics, (iv) improved support for immunogenomics and immunotherapy, and (v) new visualization and analysis features for understanding response to therapy.

(3) New analysis and target discovery features for large cohorts, including (i) supporting user-defined virtual cohort by selecting samples from multiple studies, and (ii) comparison of genomic or clinical characteristics of two or more selected cohorts.

(4) Expanding community outreach, user support and training, and documentation.

Citation Format: Jianjiong Gao, Ersin Ciftci, Pichai Raman, Pieter Lukasse, Istemi Bahceci, Adam Abeshouse, Hsiao-Wei Chen, Ino de Bruijn, Benjamin Gross, Zachary Heins, Ritika Kundra, Aaron Lisman, Angelica Ochoa, Robert Sheridan, Onur Sumer, Yichao Sun, Jiaojiao Wang, Manda Wilson, Hongxin Zhang, James Xu, Andy Dufilie, Priti Kumari, James Lindsay, Anthony Cros, Karthik Kalletla, Fedde Schaeffer, Sander Tan, Sjoerd van Hagen, Jorge Reis-Filho, Kees van Bochove, Ugur Dogrusoz, Trevor Pugh, Adam Resnick, Chris Sander, Ethan Cerami, Nikolaus Schultz. The cBioPortal for Cancer Genomics: an open source platform for accessing and interpreting complex cancer genomics data in the era of precision medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2607. doi:10.1158/1538-7445.AM2017-2607

Abstract 5277: The cBioPortal for cancer genomics and its application in precision oncology

The cBioPortal for Cancer Genomics provides intuitive visualization and analysis of complex cancer genomics data. The public site (http://cbioportal.org/) is accessed by more than 1,500 researchers per day, and there are now dozens of local instances of the software that host private data sets at cancer centers around the globe.

We have recently released the software under an open source license, making it free to use and modify by anybody. The software and detailed documentation are available at https://github.com/cBioPortal/cbioportal.

We are now establishing a multi-institutional software development network, which will coordinate and drive the future development of the software and associated data pipelines. This group will focus on four main areas:

1. New analysis and visualization features, including:

a. Improved support for cross-cancer queries and cohort comparisons.

b. Enhanced clinical decision support for precision oncology, including an improved patient view with knowledge base integration, patient timelines and improved tools for visualizing tumor evolution.

2. New data pipelines, including support for new genomic data types and streamlined pipelines for TCGA and the International Cancer Genome Consortium (ICGC).

3. Software architecture and performance improvements.

4. Community engagement: Documentation, user support, and training.

This coordinated effort will help to further establish the cBioPortal as the software of choice in cancer genomics research, both in academia and the pharmaceutical industry. Furthermore, as the sequencing of tumor samples has entered clinical practice, we are expanding the features of the software so that it can be used for precision medicine at cancer centers. In particular, clean, web-accessible, interactive clinical reports integrating multiple sources of genome variation and clinical annotation over time has potential to improve clinical action beyond current text-based molecular reports. By making complex genomic data easily interpretable and linking it to information about drugs and clinical trials, the cBioPortal software has the potential to facilitate the use of genomic data in clinical decision making.

Citation Format: Jianjiong Gao, James Lindsay, Stuart Watt, Istemi Bahceci, Pieter Lukasse, Adam Abeshouse, Hsiao-Wei Chen, Ino de Bruijn, Benjamin Gross, Dong Li, Ritika Kundra, Zachary Heins, Jorge Reis-Filho, Onur Sumer, Yichao Sun, Jiaojiao Wang, Qingguo Wang, Hongxin Zhang, Priti Kumari, M. Furkan Sahin, Sander de Ridder, Fedde Schaeffer, Kees van Bochove, Ugur Dogrusoz, Trevor Pugh, Chris Sander, Ethan Cerami, Nikolaus Schultz. The cBioPortal for cancer genomics and its application in precision oncology. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5277.

Cytoscape.js: a graph theory library for visualisation and analysis

Summary: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js.

Availability and implementation: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org.

Contact:gary.bader@utoronto.ca

Effect of sildenafil citrate on secondary healing in full thickness skin defects in experiment

OBJECTIVES

An acceleration of the wound healing process expedites chronic wound patient's return to normal social environments significantly. Sildenafil, a cyclic guanosine monophosphate (cGMP)-dependent phosphodiesterase- 5 inhibitor has been shown to be a potent stimulator of angiogenesis through upregulation of cGMP. In our study, sildenafil was administered orally as a cost-effective supplement in the treatment of full thickness defects and chronic wounds in that manner with low incidence of side effects and morbidity.

MATERIALS AND METHODS

Randomly selected 72 Wistar-Albino rats were divided into the two groups, 36 rats in each group. Control group (n =36) was divided further into a secondary healing group consisting of 9 rats and a pathology group consisting of 27 rats (pathology group 1: 9 rats, 4th and 7th day of wound healing, pathology group 2: 9 rats, 10th and 14th day of wound healing, pathology group 3: 9 rats, 21st and 28th day of wound healing. Experimental group consisted of 36 rats which received sildenafil citrate (Viagra® Pfizer, Germany) for secondary wound healing to proceed.

RESULTS

The average wound healing period in the control group was 17.89 days and in the sildenafil citrate administered group 14.56 days. The difference of the epithelialisation on full thickness defects were more prominent on days 5 and 11 postoperatively. In the sildenafil citrate applied group, on the 7th day, the defect was 25% smaller and on the 13th day, the defect contracted by 38%.

CONCLUSION

In conclusion, we believe that sildenafil citrate administered orally is a cost- effective supplement in the treatment of full thickness defects and chronic wounds in that manner with low incidence of side effects and morbidity (Tab. 4, Fig. 7, Ref. 34).